
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/00498/20/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/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/READ-TP/3472493/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/3352996/READ-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=READ-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=READ-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=336, 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"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                4               158 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                4               158 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               27               135 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               27               135 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               20               142 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               20               142 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               21               141 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               21               141 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               17               145 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               17               145 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               23               139 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               23               139 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               158 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               158 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               159 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               159 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               20               142 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               20               142 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               12               150 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               12               150 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               27               135 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               27               135 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               27               135 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               27               135 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               90                72 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               90                72 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               79                83 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               79                83 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               27               135 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               27               135 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               72                90 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               72                90 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
               35               127 
      9P GAIN CNV 9P GAIN WILD-TYPE 
               35               127 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               26               136 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               26               136 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 8                154 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 8                154 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                158 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                158 
[1] "11p gain"
[1] 3
      11P GAIN CNV 11P GAIN WILD-TYPE 
                21                141 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                21                141 
[1] "11q gain"
[1] 3
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                17                145 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                17                145 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                28                134 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                28                134 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                19                143 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                19                143 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
               102                 60 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
               102                 60 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                158 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                158 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                29                133 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                29                133 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                30                132 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                30                132 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                159 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                159 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                18                144 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                18                144 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                155 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 7                155 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                158 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                158 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                20                142 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                20                142 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                23                139 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                23                139 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                95                 67 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                95                 67 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
               132                 30 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
               132                 30 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 7                155 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 7                155 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                157 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                157 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                7               155 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                7               155 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               21               141 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               21               141 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                7               155 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                7               155 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                5               157 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                5               157 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8               154 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                8               154 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4               158 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                4               158 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               39               123 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               39               123 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               46               116 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               46               116 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               151 
      5P LOSS CNV 5P LOSS WILD-TYPE 
               11               151 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               23               139 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               23               139 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                8               154 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                8               154 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               14               148 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               14               148 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               56               106 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               56               106 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                3               159 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                3               159 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               12               150 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               12               150 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               11               151 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               11               151 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                17                145 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                17                145 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                21                141 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                21                141 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                19                143 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                19                143 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                23                139 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                23                139 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                12                150 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                12                150 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 8                154 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 8                154 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 5                157 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 5                157 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                51                111 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                51                111 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                58                104 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                58                104 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 6                156 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 6                156 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                10                152 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                10                152 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                89                 73 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                89                 73 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                15                147 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                15                147 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
               114                 48 
      18P LOSS CNV 18P LOSS WILD-TYPE 
               114                 48 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               126                 36 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               126                 36 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 7                155 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 7                155 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 7                155 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 7                155 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                18                144 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                18                144 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                43                119 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                43                119 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                42                120 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                42                120 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                6               156 
      XQ LOSS CNV 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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 162 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         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          365           NA           NA 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
          31           31           61           NA           31           31 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           NA           NA           NA           NA           30 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
          NA           NA           NA           30           NA           NA 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
          NA           NA           NA          242           29           NA 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
          31           NA           30           30           NA           NA 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
          31           NA           28           NA           31           30 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
          30           31           NA           NA           NA           NA 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 
          31           31           NA           31           31           NA 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
          NA           30          637          423          183          789 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
         700          518          484          396           31           31 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
         365          365         2130         1946          334           NA 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1519           NA           NA         1884         1246         1156 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
          15           44           21           22          140           55 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
         310          183          183           NA          211          285 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
         143          425         1825          243          334          335 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
         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=93,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "GENDER"                                
 [3] "HISTOLOGICAL.TYPE"                     
 [4] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [5] "DISTANT.METASTASIS"                    
 [6] "LYMPH.NODE.METASTASIS"                 
 [7] "COMPLETENESS.OF.RESECTION"             
 [8] "NUMBER.OF.LYMPH.NODES"                 
 [9] "TUMOR.STAGECODE"                       
[10] "NEOPLASM.DISEASESTAGE"                 
[1] "TUMOR.?STAGE" "9"           
[1] "stage2"
vv
 T1  T2  T3  T4 T4A T4B 
  9  29 109   5   8   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 162 columns, 1 survival variables, and 10 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
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN CNV         2   1
  1P GAIN WILD-TYPE 117  10
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3               127 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1                10 
$`1P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-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-F5-6465 TCGA-F5-6571 
        2.73         5.23         7.79         2.76         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 

      1P GAIN CNV 1P GAIN WILD-TYPE 
             1.02              0.16 
      1P GAIN CNV 1P GAIN WILD-TYPE 
            24.13            121.08 
      1P GAIN CNV 1P GAIN WILD-TYPE 
             2.04              6.35 
[1] "1.0 - 24.1 (2.0)"  "0.2 - 121.1 (6.3)"
       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-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE" "1P GAIN 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-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE" "1P GAIN 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-3575        TCGA-AG-3581 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "10" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    1
  1P GAIN WILD-TYPE   71   87
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  FEMALE           3                71
  MALE             1                87
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    1
  1P GAIN WILD-TYPE  140   12
                                clus
vv                               1P GAIN CNV 1P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    3               140
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D1V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          0    4
  1P GAIN WILD-TYPE    6  152
     clus
vv    1P GAIN CNV 1P GAIN WILD-TYPE
  NO            0                 6
  YES           4               152
                   vv
clus                 M0  M1 M1A  MX
  1P GAIN CNV         4   0   0   0
  1P GAIN WILD-TYPE 119  22   2  13
D1V6, multiclass
     clus
vv    1P GAIN CNV 1P GAIN WILD-TYPE
  M0            4               119
  M1            0                22
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  1P GAIN CNV        1  0   0   0   0  1   1   1  0
  1P GAIN WILD-TYPE 82 35   4   5   1 22   1   6  1
D1V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  1P GAIN CNV         3   0   0   0
  1P GAIN WILD-TYPE 118   2  12   3
D1V8, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  R0           3               118
  R1           0                 2
  R2           0                12
  RX           0                 3
D1V9, continuous
D1V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P GAIN CNV             1        0         0         0         0         0
  1P GAIN WILD-TYPE      29        8        38         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P GAIN CNV                0          0          2        0         1
  1P GAIN WILD-TYPE          9         23         11       17         8
D1V11, multiclass

Clustering(2) Variable = 1q gain
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN CNV        18   3
  1Q GAIN WILD-TYPE 101   8
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               21               109 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                3                 8 
$`1Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 
       12.00         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
        1.02        12.00        63.98        10.98        49.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.94        40.96         1.45         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01         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-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-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-6883 TCGA-EI-6884 TCGA-EI-6917 
        6.90         7.10         6.15         3.98         2.73         7.79 
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-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.53         1.08         0.46        18.25        47.70 
TCGA-G5-6572 
       47.08 

      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             0.49              0.16 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
            70.03            121.08 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             5.23              6.35 
[1] "0.5 - 70.0 (5.2)"  "0.2 - 121.1 (6.3)"
       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 CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       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 CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       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 CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
[1] "hr=" "1.7"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV         14   13
  1Q GAIN WILD-TYPE   60   75
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  FEMALE          14                60
  MALE            13                75
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV         22    4
  1Q GAIN WILD-TYPE  121    9
                                clus
vv                               1Q GAIN CNV 1Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   22               121
  RECTAL MUCINOUS ADENOCARCINOMA           4                 9
D2V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          1   26
  1Q GAIN WILD-TYPE    5  130
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  NO            1                 5
  YES          26               130
                   vv
clus                 M0  M1 M1A  MX
  1Q GAIN CNV        20   4   0   3
  1Q GAIN WILD-TYPE 103  18   2  10
D2V6, multiclass
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  M0           20               103
  M1            4                18
  M1A           0                 2
  MX            3                10
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  1Q GAIN CNV       12  4   0   1   0  5   1   3  1
  1Q GAIN WILD-TYPE 71 31   4   4   1 18   1   4  0
D2V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN CNV        19   1   2   0
  1Q GAIN WILD-TYPE 102   1  10   3
D2V8, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  R0          19               102
  R1           1                 1
  R2           2                10
  RX           0                 3
D2V9, continuous
D2V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q GAIN CNV             3        2         6         0         0         0
  1Q GAIN WILD-TYPE      27        6        32         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q GAIN CNV                1          2          6        4         1
  1Q GAIN WILD-TYPE          8         21          7       13         8
D2V11, multiclass

Clustering(3) Variable = 2p gain
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN CNV        15   2
  2P GAIN WILD-TYPE 104   9
      2P GAIN CNV 2P GAIN WILD-TYPE 
               17               113 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                2                 9 
$`2P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-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-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-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01         9.99         5.03         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-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      119.51        41.33        57.24        24.13        32.58         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40         0.16         2.17         8.22         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        0.66         6.90         6.15         3.55         3.98         2.73 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
        5.23         7.79         2.76         2.04         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-G5-6641 
        0.76         0.46        18.25        47.70        20.91 

      2P GAIN CNV 2P GAIN WILD-TYPE 
             1.02              0.16 
      2P GAIN CNV 2P GAIN WILD-TYPE 
           121.08            119.51 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            10.98              5.23 
[1] "1.0 - 121.1 (11.0)" "0.2 - 119.5 (5.2)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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 CNV" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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 CNV" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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 CNV" "2P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV         15    5
  2P GAIN WILD-TYPE   59   83
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  FEMALE          15                59
  MALE             5                83
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV         20    0
  2P GAIN WILD-TYPE  123   13
                                clus
vv                               2P GAIN CNV 2P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   20               123
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D3V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          0   20
  2P GAIN WILD-TYPE    6  136
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  NO            0                 6
  YES          20               136
                   vv
clus                 M0  M1 M1A  MX
  2P GAIN CNV        12   5   0   2
  2P GAIN WILD-TYPE 111  17   2  11
D3V6, multiclass
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  M0           12               111
  M1            5                17
  M1A           0                 2
  MX            2                11
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  2P GAIN CNV       10  2   1   0   0  4   1   1  0
  2P GAIN WILD-TYPE 73 33   3   5   1 19   1   6  1
D3V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  2P GAIN CNV        13   0   2   2
  2P GAIN WILD-TYPE 108   2  10   1
D3V8, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  R0          13               108
  R1           0                 2
  R2           2                10
  RX           2                 1
D3V9, continuous
D3V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P GAIN CNV             2        2         5         0         0         0
  2P GAIN WILD-TYPE      28        6        33         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P GAIN CNV                0          2          3        3         2
  2P GAIN WILD-TYPE          9         21         10       14         7
D3V11, multiclass

Clustering(4) Variable = 2q gain
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN CNV        16   1
  2Q GAIN WILD-TYPE 103  10
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               17               113 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                1                10 
$`2Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02         1.02        12.00        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.94         1.94        38.93        61.94        40.96         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         0.72         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        6.02         6.94         9.37         4.70        13.97        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01         9.99         5.03         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-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      119.51        41.33        57.24        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-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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.08         0.46        18.25        47.70        20.91 

      2Q GAIN CNV 2Q GAIN WILD-TYPE 
             0.76              0.16 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
           121.08            119.51 
      2Q GAIN CNV 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 CNV" "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 CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "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 CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "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 CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
[1] "hr=" "4"  
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV         15    6
  2Q GAIN WILD-TYPE   59   82
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  FEMALE          15                59
  MALE             6                82
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV         21    0
  2Q GAIN WILD-TYPE  122   13
                                clus
vv                               2Q GAIN CNV 2Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   21               122
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D4V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          0   21
  2Q GAIN WILD-TYPE    6  135
     clus
vv    2Q GAIN CNV 2Q GAIN WILD-TYPE
  NO            0                 6
  YES          21               135
                   vv
clus                 M0  M1 M1A  MX
  2Q GAIN CNV        14   4   0   2
  2Q GAIN WILD-TYPE 109  18   2  11
D4V6, multiclass
     clus
vv    2Q GAIN CNV 2Q GAIN WILD-TYPE
  M0           14               109
  M1            4                18
  M1A           0                 2
  MX            2                11
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  2Q GAIN CNV       11  2   0   0   0  5   1   1  0
  2Q GAIN WILD-TYPE 72 33   4   5   1 18   1   6  1
D4V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN CNV        15   0   2   2
  2Q GAIN WILD-TYPE 106   2  10   1
D4V8, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  R0          15               106
  R1           0                 2
  R2           2                10
  RX           2                 1
D4V9, continuous
D4V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q GAIN CNV             2        2         6         0         0         0
  2Q GAIN WILD-TYPE      28        6        32         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q GAIN CNV                0          2          4        3         1
  2Q GAIN WILD-TYPE          9         21          9       14         8
D4V11, multiclass

Clustering(5) Variable = 3p gain
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN CNV        11   1
  3P GAIN WILD-TYPE 108  10
      3P GAIN CNV 3P GAIN WILD-TYPE 
               12               118 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                10 
$`3P GAIN CNV`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3896 TCGA-DC-4745 TCGA-DC-5869 
       17.62         6.35         7.33         1.02        10.98         5.03 
TCGA-DC-6156 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 
        6.97        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-3575 
       12.72        10.39        14.50         8.45         7.59        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-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-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.70        13.97        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        9.99         8.98         7.36        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
        5.92         3.98         5.00         0.26       119.51        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-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-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-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 

      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.46              0.16 
      3P GAIN CNV 3P GAIN WILD-TYPE 
           121.08            119.51 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            6.660             6.085 
[1] "0.5 - 121.1 (6.7)" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          8    9
  3P GAIN WILD-TYPE   66   79
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  FEMALE           8                66
  MALE             9                79
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV         17    0
  3P GAIN WILD-TYPE  126   13
                                clus
vv                               3P GAIN CNV 3P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   17               126
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D5V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          2   15
  3P GAIN WILD-TYPE    4  141
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  NO            2                 4
  YES          15               141
                   vv
clus                 M0  M1 M1A  MX
  3P GAIN CNV        11   2   1   3
  3P GAIN WILD-TYPE 112  20   1  10
D5V6, multiclass
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  M0           11               112
  M1            2                20
  M1A           1                 1
  MX            3                10
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  3P GAIN CNV        8  1   2   0   0  4   0   2  0
  3P GAIN WILD-TYPE 75 34   2   5   1 19   2   5  1
D5V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  3P GAIN CNV        13   0   0   0
  3P GAIN WILD-TYPE 108   2  12   3
D5V8, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  R0          13               108
  R1           0                 2
  R2           0                12
  RX           0                 3
D5V9, continuous
D5V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P GAIN CNV             1        0         6         0         0         1
  3P GAIN WILD-TYPE      29        8        32         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P GAIN CNV                1          2          1        3         2
  3P GAIN WILD-TYPE          8         21         12       14         7
D5V11, multiclass

Clustering(6) Variable = 3q gain
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN CNV        14   2
  3Q GAIN WILD-TYPE 105   9
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               16               114 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2                 9 
$`3Q GAIN CNV`
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3726 TCGA-AG-3896 
       17.62        10.39         6.35         7.33         7.96         1.02 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DY-A1DC TCGA-EF-5831 
       60.00        10.98         5.03         6.97        41.33         2.40 
TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6863 
        0.46         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-3575 TCGA-AG-3581 
       12.72        14.50         8.45         7.59        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-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-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       13.97         7.99        11.01         9.99         8.98         7.36 
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-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        0.26       119.51        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-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-7004 TCGA-F5-6465 TCGA-F5-6571 
        2.73         5.23         7.79         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-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.08         0.46        18.25        47.70        47.08        20.91 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
             0.46              0.16 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            60.00            121.08 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            7.035             6.020 
[1] "0.5 - 60.0 (7.0)"  "0.2 - 121.1 (6.0)"
       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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV         13   10
  3Q GAIN WILD-TYPE   61   78
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  FEMALE          13                61
  MALE            10                78
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV         23    0
  3Q GAIN WILD-TYPE  120   13
                                clus
vv                               3Q GAIN CNV 3Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   23               120
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D6V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          2   21
  3Q GAIN WILD-TYPE    4  135
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  NO            2                 4
  YES          21               135
                   vv
clus                 M0  M1 M1A  MX
  3Q GAIN CNV        15   3   1   4
  3Q GAIN WILD-TYPE 108  19   1   9
D6V6, multiclass
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  M0           15               108
  M1            3                19
  M1A           1                 1
  MX            4                 9
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  3Q GAIN CNV        9  4   3   0   0  5   0   2  0
  3Q GAIN WILD-TYPE 74 31   1   5   1 18   2   5  1
D6V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN CNV        19   0   0   1
  3Q GAIN WILD-TYPE 102   2  12   2
D6V8, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  R0          19               102
  R1           0                 2
  R2           0                12
  RX           1                 2
D6V9, continuous
D6V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q GAIN CNV             2        0         6         0         0         1
  3Q GAIN WILD-TYPE      28        8        32         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q GAIN CNV                1          5          2        3         2
  3Q GAIN WILD-TYPE          8         18         11       14         7
D6V11, multiclass

Clustering(7) Variable = 4p gain
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN CNV         3   1
  4P GAIN WILD-TYPE 116  10
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               126 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                10 
$`4P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-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-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        10.98         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-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      121.08        24.13        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-F5-6465 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 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             0.46              0.16 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            51.48            121.08 
      4P GAIN CNV 4P GAIN WILD-TYPE 
           14.020             6.085 
[1] "0.5 - 51.5 (14.0)" "0.2 - 121.1 (6.1)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          1    3
  4P GAIN WILD-TYPE   73   85
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           1                73
  MALE             3                85
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          4    0
  4P GAIN WILD-TYPE  139   13
                                clus
vv                               4P GAIN CNV 4P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    4               139
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D7V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    4
  4P GAIN WILD-TYPE    6  152
     clus
vv    4P GAIN CNV 4P GAIN WILD-TYPE
  NO            0                 6
  YES           4               152
                   vv
clus                 M0  M1 M1A  MX
  4P GAIN CNV         2   1   0   1
  4P GAIN WILD-TYPE 121  21   2  12
D7V6, multiclass
     clus
vv    4P GAIN CNV 4P GAIN WILD-TYPE
  M0            2               121
  M1            1                21
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  4P GAIN CNV        3  1   0   0   0  0   0   0  0
  4P GAIN WILD-TYPE 80 34   4   5   1 23   2   7  1
D7V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  4P GAIN CNV         3   0   0   0
  4P GAIN WILD-TYPE 118   2  12   3
D7V8, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  R0           3               118
  R1           0                 2
  R2           0                12
  RX           0                 3
D7V9, continuous
D7V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P GAIN CNV             1        0         1         0         0         0
  4P GAIN WILD-TYPE      29        8        37         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P GAIN CNV                0          0          0        0         2
  4P GAIN WILD-TYPE          9         23         13       17         7
D7V11, multiclass

Clustering(8) Variable = 4q gain
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN CNV         1   1
  4Q GAIN WILD-TYPE 118  10
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               128 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                1                10 
$`4Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.02         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.00         7.99        10.98        11.01         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-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 

      4Q GAIN CNV 4Q GAIN WILD-TYPE 
             0.99              0.16 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
            51.48            121.08 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
           26.235             6.250 
[1] "1.0 - 51.5 (26.2)" "0.2 - 121.1 (6.2)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               128 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3894        TCGA-AG-3896 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007        TCGA-AG-4008 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J        TCGA-AG-A01L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AH-6544 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-4957 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-7004        TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          0    3
  4Q GAIN WILD-TYPE   74   85
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  FEMALE           0                74
  MALE             3                85
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          3    0
  4Q GAIN WILD-TYPE  140   13
                                clus
vv                               4Q GAIN CNV 4Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    3               140
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D8V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          0    3
  4Q GAIN WILD-TYPE    6  153
     clus
vv    4Q GAIN CNV 4Q GAIN WILD-TYPE
  NO            0                 6
  YES           3               153
                   vv
clus                 M0  M1 M1A  MX
  4Q GAIN CNV         2   1   0   0
  4Q GAIN WILD-TYPE 121  21   2  13
D8V6, multiclass
     clus
vv    4Q GAIN CNV 4Q GAIN WILD-TYPE
  M0            2               121
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  4Q GAIN CNV        1  2   0   0   0  0   0   0  0
  4Q GAIN WILD-TYPE 82 33   4   5   1 23   2   7  1
D8V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN CNV         2   0   0   0
  4Q GAIN WILD-TYPE 119   2  12   3
D8V8, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2               136 
       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-3400        TCGA-AF-3913        TCGA-AF-4110 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3578        TCGA-AG-3580        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-3584        TCGA-AG-3586        TCGA-AG-3587 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3591        TCGA-AG-3592        TCGA-AG-3593        TCGA-AG-3594 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3725        TCGA-AG-3726 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3728        TCGA-AG-3731        TCGA-AG-3732 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3885        TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-4021 
"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-6643 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-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-EF-5830 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "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-F5-6464        TCGA-F5-6465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6812 
"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-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V9, continuous
D8V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q GAIN CNV             0        0         1         0         0         0
  4Q GAIN WILD-TYPE      30        8        37         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q GAIN CNV                0          1          0        0         1
  4Q GAIN WILD-TYPE          9         22         13       17         8
D8V11, multiclass

Clustering(9) Variable = 5p gain
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN CNV        17   1
  5P GAIN WILD-TYPE 102  10
      5P GAIN CNV 5P GAIN WILD-TYPE 
               18               112 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                1                10 
$`5P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 
        7.33        12.00         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.94        23.01        17.03        15.91         1.02 
TCGA-AG-A01J TCGA-AG-A01L 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-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       49.94         1.94        61.94         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01         9.99         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-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-6881 TCGA-EI-6882 TCGA-EI-6884 
        3.98         0.66         6.90         6.15         3.55         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-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.39         0.66         0.69         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 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             0.72              0.16 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            40.96            121.08 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            4.505             6.625 
[1] "0.7 - 41.0 (4.5)"  "0.2 - 121.1 (6.6)"
       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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          8   12
  5P GAIN WILD-TYPE   66   76
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  FEMALE           8                66
  MALE            12                76
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV         20    0
  5P GAIN WILD-TYPE  123   13
                                clus
vv                               5P GAIN CNV 5P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   20               123
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D9V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          1   19
  5P GAIN WILD-TYPE    5  137
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  NO            1                 5
  YES          19               137
                   vv
clus                 M0  M1 M1A  MX
  5P GAIN CNV        13   5   0   2
  5P GAIN WILD-TYPE 110  17   2  11
D9V6, multiclass
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  M0           13               110
  M1            5                17
  M1A           0                 2
  MX            2                11
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  5P GAIN CNV        9  6   1   0   0  3   0   0  1
  5P GAIN WILD-TYPE 74 29   3   5   1 20   2   7  0
D9V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  5P GAIN CNV        13   0   4   0
  5P GAIN WILD-TYPE 108   2   8   3
D9V8, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  R0          13               108
  R1           0                 2
  R2           4                 8
  RX           0                 3
D9V9, continuous
D9V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P GAIN CNV             4        0         3         0         1         0
  5P GAIN WILD-TYPE      26        8        35         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P GAIN CNV                0          4          2        4         1
  5P GAIN WILD-TYPE          9         19         11       13         8
D9V11, multiclass

Clustering(10) Variable = 5q gain
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN CNV        10   0
  5Q GAIN WILD-TYPE 109  11
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               10               120 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                0                11 
$`5Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-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-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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       61.94         0.49         1.45         0.69         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-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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        2.73         5.23         7.79         2.04         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        2.17         0.39         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 

      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             0.72              0.16 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            40.96            121.08 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            3.370             6.625 
[1] "0.7 - 41.0 (3.4)"  "0.2 - 121.1 (6.6)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          5    7
  5Q GAIN WILD-TYPE   69   81
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  FEMALE           5                69
  MALE             7                81
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV         12    0
  5Q GAIN WILD-TYPE  131   13
                                clus
vv                               5Q GAIN CNV 5Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   12               131
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D10V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          0   12
  5Q GAIN WILD-TYPE    6  144
     clus
vv    5Q GAIN CNV 5Q GAIN WILD-TYPE
  NO            0                 6
  YES          12               144
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN CNV         7   4   0   1
  5Q GAIN WILD-TYPE 116  18   2  12
D10V6, multiclass
     clus
vv    5Q GAIN CNV 5Q GAIN WILD-TYPE
  M0            7               116
  M1            4                18
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  5Q GAIN CNV        5  3   0   0   0  3   0   0  1
  5Q GAIN WILD-TYPE 78 32   4   5   1 20   2   7  0
D10V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN CNV         7   0   3   0
  5Q GAIN WILD-TYPE 114   2   9   3
D10V8, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  R0           7               114
  R1           0                 2
  R2           3                 9
  RX           0                 3
D10V9, continuous
D10V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q GAIN CNV             1        0         2         0         1         0
  5Q GAIN WILD-TYPE      29        8        36         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q GAIN CNV                0          2          1        4         0
  5Q GAIN WILD-TYPE          9         21         12       13         9
D10V11, multiclass

Clustering(11) Variable = 6p gain
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN CNV       20  1
  6P GAIN WILD-TYPE 99 10
      6P GAIN CNV 6P GAIN WILD-TYPE 
               21               109 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                1                10 
$`6P GAIN CNV`
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-3883 TCGA-AG-3896 
       19.53        17.62        10.39         7.59         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 
        1.02         0.99        13.02         1.02        12.00         0.72 
TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EI-6511 
        9.37         5.03         8.98        27.91       121.08         3.98 
TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6810 
        0.66         3.39         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-3575 TCGA-AG-3581 
       14.50         8.45         6.35         7.33        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.96         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-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-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.91         1.02        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-6897 TCGA-AH-6903 
       38.01         0.49         1.45         0.69         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-6155 
       60.00         7.99        10.98        11.01         9.99         7.36 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        6.97         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-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        8.22         0.46         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-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        0.85         2.17         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 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             0.39              0.16 
      6P GAIN CNV 6P GAIN WILD-TYPE 
           121.08            119.51 
      6P GAIN CNV 6P GAIN WILD-TYPE 
             5.03              6.35 
[1] "0.4 - 121.1 (5.0)" "0.2 - 119.5 (6.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV         13   14
  6P GAIN WILD-TYPE   61   74
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  FEMALE          13                61
  MALE            14                74
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV         27    0
  6P GAIN WILD-TYPE  116   13
                                clus
vv                               6P GAIN CNV 6P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   27               116
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D11V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          3   24
  6P GAIN WILD-TYPE    3  132
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  NO            3                 3
  YES          24               132
                   vv
clus                 M0  M1 M1A  MX
  6P GAIN CNV        18   6   0   3
  6P GAIN WILD-TYPE 105  16   2  10
D11V6, multiclass
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  M0           18               105
  M1            6                16
  M1A           0                 2
  MX            3                10
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  6P GAIN CNV       11  5   2   1   0  6   0   1  1
  6P GAIN WILD-TYPE 72 30   2   4   1 17   2   6  0
D11V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  6P GAIN CNV        17   0   5   0
  6P GAIN WILD-TYPE 104   2   7   3
D11V8, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  R0          17               104
  R1           0                 2
  R2           5                 7
  RX           0                 3
D11V9, continuous
D11V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P GAIN CNV             5        1         4         0         0         1
  6P GAIN WILD-TYPE      25        7        34         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P GAIN CNV                0          7          2        4         1
  6P GAIN WILD-TYPE          9         16         11       13         8
D11V11, multiclass

Clustering(12) Variable = 6q gain
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN CNV        19   2
  6Q GAIN WILD-TYPE 100   9
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
               21               109 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                 9 
$`6Q GAIN CNV`
TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3883 TCGA-AG-3896 
       19.53        10.39        14.50         7.59         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AH-6644 
        1.02         0.99        13.02         1.02        12.00         0.72 
TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6511 
        9.37         5.03         8.98        27.91        51.48         3.98 
TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6810 
        0.66         3.39         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-3575 TCGA-AG-3581 
       17.62         8.45         6.35         7.33        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.96         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-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-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.91         1.02        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-6897 TCGA-AH-6903 
       38.01         0.49         1.45         0.69         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-6155 
       60.00         7.99        10.98        11.01         9.99         7.36 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        6.97         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-A1DF 
        0.26       119.51        41.33        57.24       121.08        24.13 
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-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        8.22         0.46         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-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        0.85         2.17         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 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             0.39              0.16 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            51.48            121.08 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             5.03              6.35 
[1] "0.4 - 51.5 (5.0)"  "0.2 - 121.1 (6.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6Q GAIN CNV" "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 CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6Q GAIN CNV" "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 CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "6Q GAIN CNV" "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 CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV         12   15
  6Q GAIN WILD-TYPE   62   73
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  FEMALE          12                62
  MALE            15                73
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV         26    0
  6Q GAIN WILD-TYPE  117   13
                                clus
vv                               6Q GAIN CNV 6Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   26               117
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D12V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          2   25
  6Q GAIN WILD-TYPE    4  131
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  NO            2                 4
  YES          25               131
                   vv
clus                 M0  M1 M1A  MX
  6Q GAIN CNV        17   7   0   3
  6Q GAIN WILD-TYPE 106  15   2  10
D12V6, multiclass
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  M0           17               106
  M1            7                15
  M1A           0                 2
  MX            3                10
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  6Q GAIN CNV       10  6   2   1   0  5   0   2  1
  6Q GAIN WILD-TYPE 73 29   2   4   1 18   2   5  0
D12V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN CNV        18   0   5   0
  6Q GAIN WILD-TYPE 103   2   7   3
D12V8, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  R0          18               103
  R1           0                 2
  R2           5                 7
  RX           0                 3
D12V9, continuous
D12V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q GAIN CNV             5        1         3         0         0         1
  6Q GAIN WILD-TYPE      25        7        35         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q GAIN CNV                0          7          1        4         3
  6Q GAIN WILD-TYPE          9         16         12       13         6
D12V11, multiclass

Clustering(13) Variable = 7p gain
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV       66  8
  7P GAIN WILD-TYPE 53  3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               74                56 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                8                 3 
$`7P GAIN CNV`
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-3605 
        7.59         6.35         1.02         1.02         1.02         0.99 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
        0.99        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 
       70.03         1.94        38.93        38.01         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        4.60        10.19         6.02         9.37         4.70        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        7.99        10.98        11.01         5.03         8.98         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       27.91         6.97         5.00         0.26       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
       57.24       121.08        24.13         0.49         2.40         2.17 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
        0.46         3.98         0.66         6.90         7.10         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6810 
        2.73         5.23         2.76         2.04         2.17         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 
       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-3575 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
       12.00         2.01         1.02         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3999 
        1.02         1.02         0.92         1.02         0.99         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       17.03        12.00        63.98        10.98        51.98        49.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
       61.94        40.96         0.49         1.45         1.81         6.02 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 
        6.94        13.97         9.99         7.36        19.99         5.92 
TCGA-DC-6682 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
        3.98        51.48        32.58         7.63         0.16         8.22 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6814 
        6.15         3.55         7.79         3.39         0.85         0.53 
TCGA-F5-6861 TCGA-G5-6641 
        1.08        20.91 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             0.26              0.16 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           121.08             63.98 
      7P GAIN CNV 7P GAIN WILD-TYPE 
            5.015             7.495 
[1] "0.3 - 121.1 (5.0)" "0.2 - 64.0 (7.5)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         42   48
  7P GAIN WILD-TYPE   32   40
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE          42                32
  MALE            48                40
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         87    2
  7P GAIN WILD-TYPE   56   11
                                clus
vv                               7P GAIN CNV 7P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   87                56
  RECTAL MUCINOUS ADENOCARCINOMA           2                11
D13V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          3   87
  7P GAIN WILD-TYPE    3   69
     clus
vv    7P GAIN CNV 7P GAIN WILD-TYPE
  NO            3                 3
  YES          87                69
                   vv
clus                M0 M1 M1A MX
  7P GAIN CNV       65 14   1  8
  7P GAIN WILD-TYPE 58  8   1  5
D13V6, multiclass
     clus
vv    7P GAIN CNV 7P GAIN WILD-TYPE
  M0           65                58
  M1           14                 8
  M1A           1                 1
  MX            8                 5
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  7P GAIN CNV       39 20   4   3   1 15   1   5  1
  7P GAIN WILD-TYPE 44 15   0   2   0  8   1   2  0
D13V7, multiclass
                   vv
clus                R0 R1 R2 RX
  7P GAIN CNV       64  2  8  3
  7P GAIN WILD-TYPE 57  0  4  0
D13V8, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  R0          64                57
  R1           2                 0
  R2           8                 4
  RX           3                 0
D13V9, continuous
D13V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7P GAIN CNV            15        4        16         1         2         1
  7P GAIN WILD-TYPE      15        4        22         1         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7P GAIN CNV                2         19          9       11         6
  7P GAIN WILD-TYPE          7          4          4        6         3
D13V11, multiclass

Clustering(14) Variable = 7q gain
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV       58  6
  7Q GAIN WILD-TYPE 61  5
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               64                66 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                6                 5 
$`7Q GAIN CNV`
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-3605 TCGA-AG-3742 
        6.35         1.02         1.02         1.02         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
        0.99        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       70.03        38.93        38.01         0.69         0.72         4.60 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       10.19         6.02         9.37        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01         5.03         8.98         6.97        27.91         6.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
        5.00         0.26        41.33        57.24        24.13         0.49 
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-6883 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        3.98         2.76         2.17         0.39         1.02         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        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-3575 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3726 
        7.33        12.00         2.01         1.02         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.95         1.02         1.02         0.92         1.02         0.99 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       17.03        12.00        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6903 
        1.94        61.94        40.96         0.49         1.45         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6155 
        6.02         6.94         4.70        13.97         9.99         7.36 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
       19.99         5.92         3.98       119.51       121.08        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 
       32.58         2.40         7.63         0.16         8.22         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-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6641 
        0.85         0.66         0.53         1.08        18.25        20.91 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             0.26              0.16 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            70.03            121.08 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            5.015             7.345 
[1] "0.3 - 70.0 (5.0)"  "0.2 - 121.1 (7.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         36   43
  7Q GAIN WILD-TYPE   38   45
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE          36                38
  MALE            43                45
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         77    1
  7Q GAIN WILD-TYPE   66   12
                                clus
vv                               7Q GAIN CNV 7Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   77                66
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D14V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          3   76
  7Q GAIN WILD-TYPE    3   80
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  NO            3                 3
  YES          76                80
                   vv
clus                M0 M1 M1A MX
  7Q GAIN CNV       55 13   1  8
  7Q GAIN WILD-TYPE 68  9   1  5
D14V6, multiclass
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0           55                68
  M1           13                 9
  M1A           1                 1
  MX            8                 5
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  7Q GAIN CNV       32 19   4   2   1 14   1   4  1
  7Q GAIN WILD-TYPE 51 16   0   3   0  9   1   3  0
D14V7, multiclass
                   vv
clus                R0 R1 R2 RX
  7Q GAIN CNV       57  1  8  3
  7Q GAIN WILD-TYPE 64  1  4  0
D14V8, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  R0          57                64
  R1           1                 1
  R2           8                 4
  RX           3                 0
D14V9, continuous
D14V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q GAIN CNV            14        3        11         1         1         1
  7Q GAIN WILD-TYPE      16        5        27         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q GAIN CNV                1         19         10       10         5
  7Q GAIN WILD-TYPE          8          4          3        7         4
D14V11, multiclass

Clustering(15) Variable = 8p gain
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN CNV        18   4
  8P GAIN WILD-TYPE 101   7
      8P GAIN CNV 8P GAIN WILD-TYPE 
               22               108 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                 7 
$`8P GAIN CNV`
TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 
        6.35         1.02         0.92         1.02         1.02         0.99 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 
        1.02        12.00        63.98        38.01         0.69         0.72 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EI-6509 
        9.37         7.99        41.33        57.24        24.13         8.22 
TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6863 TCGA-G5-6572 
        3.98         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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        1.02         0.99         0.99         7.96         0.95         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        0.99         1.02         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        17.03        15.91        13.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       61.94        40.96         0.49         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-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.00        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-A1DE TCGA-DY-A1DG 
        3.98         5.00         0.26       119.51       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-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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        3.55         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 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             0.69              0.16 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            63.98            121.08 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            5.165             6.525 
[1] "0.7 - 64.0 (5.2)"  "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-3575        TCGA-AG-3581 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8P GAIN CNV" "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-3575        TCGA-AG-3581 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8P GAIN CNV" "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-3575        TCGA-AG-3581 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV"       "8P GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV         13   14
  8P GAIN WILD-TYPE   61   74
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE          13                61
  MALE            14                74
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV         25    2
  8P GAIN WILD-TYPE  118   11
                                clus
vv                               8P GAIN CNV 8P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   25               118
  RECTAL MUCINOUS ADENOCARCINOMA           2                11
D15V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          0   27
  8P GAIN WILD-TYPE    6  129
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  NO            0                 6
  YES          27               129
                   vv
clus                 M0  M1 M1A  MX
  8P GAIN CNV        19   5   0   2
  8P GAIN WILD-TYPE 104  17   2  11
D15V6, multiclass
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  M0           19               104
  M1            5                17
  M1A           0                 2
  MX            2                11
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  8P GAIN CNV       14  5   0   0   0  4   0   2  1
  8P GAIN WILD-TYPE 69 30   4   5   1 19   2   5  0
D15V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  8P GAIN CNV        15   0   5   1
  8P GAIN WILD-TYPE 106   2   7   2
D15V8, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  R0          15               106
  R1           0                 2
  R2           5                 7
  RX           1                 2
D15V9, continuous
D15V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P GAIN CNV             2        3         7         0         1         0
  8P GAIN WILD-TYPE      28        5        31         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P GAIN CNV                1          3          3        5         0
  8P GAIN WILD-TYPE          8         20         10       12         9
D15V11, multiclass

Clustering(16) Variable = 8q gain
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV       46  9
  8Q GAIN WILD-TYPE 73  2
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               55                75 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                9                 2 
$`8Q GAIN CNV`
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-3586 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3887 
        1.02         1.02         1.02         7.96         1.02         0.92 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A011 
        1.02         1.02         1.02         1.02         0.99        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.91         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       51.98         1.94        38.01         0.69         0.72         6.02 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        9.37         4.70        60.00         7.99         5.03         7.36 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        6.97         3.98         5.00        41.33        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6885 
       32.58         0.49         8.22         6.90         3.98         5.23 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        3.39         2.17         0.76        18.25        47.70        47.08 
TCGA-G5-6641 
       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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 
        7.59         7.33        12.00         1.02         2.01         0.99 
TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 
        0.99         0.95         0.99         0.99         1.02         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        0.99         0.99         1.02        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 
       25.94        23.01        13.02        12.00        10.98        49.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
       38.93        61.94        40.96         0.49         1.45         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 
        1.81        10.19         6.02         6.94        13.97        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       11.01         9.99         8.98         6.97        27.91        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 
        5.92         0.26       119.51       121.08        51.48         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-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
        7.10         6.15         3.55         2.73         7.79         2.76 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        2.04         0.85         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.53         1.08         0.46 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             0.49              0.16 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            70.03            121.08 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             6.90              6.02 
[1] "0.5 - 70.0 (6.9)"  "0.2 - 121.1 (6.0)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-G5-6572        TCGA-G5-6641 
      "8Q GAIN CNV"       "8Q GAIN CNV" 
[1] "hr=" "3.8"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         33   39
  8Q GAIN WILD-TYPE   41   49
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE          33                41
  MALE            39                49
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         67    3
  8Q GAIN WILD-TYPE   76   10
                                clus
vv                               8Q GAIN CNV 8Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   67                76
  RECTAL MUCINOUS ADENOCARCINOMA           3                10
D16V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          1   71
  8Q GAIN WILD-TYPE    5   85
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  NO            1                 5
  YES          71                85
                   vv
clus                M0 M1 M1A MX
  8Q GAIN CNV       50 14   0  7
  8Q GAIN WILD-TYPE 73  8   2  6
D16V6, multiclass
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0           50                73
  M1           14                 8
  M1A           0                 2
  MX            7                 6
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  8Q GAIN CNV       32 14   2   3   1 15   1   2  1
  8Q GAIN WILD-TYPE 51 21   2   2   0  8   1   5  0
D16V7, multiclass
                   vv
clus                R0 R1 R2 RX
  8Q GAIN CNV       47  2  9  2
  8Q GAIN WILD-TYPE 74  0  3  1
D16V8, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  R0          47                74
  R1           2                 0
  R2           9                 3
  RX           2                 1
D16V9, continuous
D16V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q GAIN CNV             9        5        15         1         2         2
  8Q GAIN WILD-TYPE      21        3        23         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q GAIN CNV                4          9          8       12         1
  8Q GAIN WILD-TYPE          5         14          5        5         8
D16V11, multiclass

Clustering(17) Variable = 9p gain
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN CNV       23  3
  9P GAIN WILD-TYPE 96  8
      9P GAIN CNV 9P GAIN WILD-TYPE 
               26               104 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3                 8 
$`9P GAIN CNV`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3587 TCGA-AG-3605 
       15.85        11.77        10.39         6.35         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A01W TCGA-AG-A020 
        7.96         0.99         1.02         1.02        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 TCGA-DY-A1DE 
       51.98        38.01         0.69         0.72        10.98       121.08 
TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6810 TCGA-F5-6813 
        2.40         3.98         2.73         2.04         0.39         0.69 
TCGA-F5-6861 TCGA-G5-6233 
        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-3575 TCGA-AG-3581 
       14.50         8.45         7.59         7.33        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 
        1.02         2.01         1.02         0.99         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-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-A01Y TCGA-AG-A025 
        1.02         1.02        12.00        12.00        63.98        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-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.70        13.97        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        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-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      119.51        41.33        57.24        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-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        5.23         7.79         2.76         3.39         0.85         2.17 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        1.02         0.66         0.53         0.76         0.46        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

      9P GAIN CNV 9P GAIN WILD-TYPE 
             0.39              0.16 
      9P GAIN CNV 9P GAIN WILD-TYPE 
           121.08            119.51 
      9P GAIN CNV 9P GAIN WILD-TYPE 
            3.355             6.920 
[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 CNV"       "9P GAIN CNV" "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 CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "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 CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "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 CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P GAIN WILD-TYPE"       "9P GAIN CNV"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV         17   18
  9P GAIN WILD-TYPE   57   70
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  FEMALE          17                57
  MALE            18                70
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV         31    3
  9P GAIN WILD-TYPE  112   10
                                clus
vv                               9P GAIN CNV 9P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   31               112
  RECTAL MUCINOUS ADENOCARCINOMA           3                10
D17V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          0   35
  9P GAIN WILD-TYPE    6  121
     clus
vv    9P GAIN CNV 9P GAIN WILD-TYPE
  NO            0                 6
  YES          35               121
                   vv
clus                M0 M1 M1A MX
  9P GAIN CNV       30  4   0  1
  9P GAIN WILD-TYPE 93 18   2 12
D17V6, multiclass
     clus
vv    9P GAIN CNV 9P GAIN WILD-TYPE
  M0           30                93
  M1            4                18
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  9P GAIN CNV       17  6   2   0   0  6   1   2  1
  9P GAIN WILD-TYPE 66 29   2   5   1 17   1   5  0
D17V7, multiclass
                   vv
clus                R0 R1 R2 RX
  9P GAIN CNV       30  0  2  0
  9P GAIN WILD-TYPE 91  2 10  3
D17V8, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  R0          30                91
  R1           0                 2
  R2           2                10
  RX           0                 3
D17V9, continuous
D17V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P GAIN CNV             4        1        10         0         2         2
  9P GAIN WILD-TYPE      26        7        28         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P GAIN CNV                3          3          3        3         1
  9P GAIN WILD-TYPE          6         20         10       14         8
D17V11, multiclass

Clustering(18) Variable = 9q gain
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN CNV        16   3
  9Q GAIN WILD-TYPE 103   8
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
               19               111 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                 8 
$`9Q GAIN CNV`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3605 TCGA-AG-3878 TCGA-AG-3896 
       15.85        10.39         6.35         0.99         0.99         1.02 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 TCGA-DY-A1DE 
       10.98        51.98        38.01         0.72        10.98       121.08 
TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 
        2.40         3.98         2.73         0.39         0.69         1.08 
TCGA-G5-6233 
       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-3575 
       17.62        14.50         8.45         7.59         7.33        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-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-A025 TCGA-AG-A026 
       12.00        12.00        70.03        63.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        40.96         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.70        13.97        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        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-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      119.51        41.33        57.24        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-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-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
        2.17         1.02         0.66         0.53         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       47.70        47.08        20.91 

      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             0.39              0.16 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
           121.08            119.51 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             3.98              6.90 
[1] "0.4 - 121.1 (4.0)" "0.2 - 119.5 (6.9)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "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 CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "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 CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "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 CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
      "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV         11   15
  9Q GAIN WILD-TYPE   63   73
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  FEMALE          11                63
  MALE            15                73
D18V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV         23    2
  9Q GAIN WILD-TYPE  120   11
                                clus
vv                               9Q GAIN CNV 9Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   23               120
  RECTAL MUCINOUS ADENOCARCINOMA           2                11
D18V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          0   26
  9Q GAIN WILD-TYPE    6  130
     clus
vv    9Q GAIN CNV 9Q GAIN WILD-TYPE
  NO            0                 6
  YES          26               130
                   vv
clus                 M0  M1 M1A  MX
  9Q GAIN CNV        21   4   0   1
  9Q GAIN WILD-TYPE 102  18   2  12
D18V6, multiclass
     clus
vv    9Q GAIN CNV 9Q GAIN WILD-TYPE
  M0           21               102
  M1            4                18
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  9Q GAIN CNV       12  5   2   0   0  5   1   0  1
  9Q GAIN WILD-TYPE 71 30   2   5   1 18   1   7  0
D18V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN CNV        21   0   2   0
  9Q GAIN WILD-TYPE 100   2  10   3
D18V8, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  R0          21               100
  R1           0                 2
  R2           2                10
  RX           0                 3
D18V9, continuous
D18V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q GAIN CNV             2        0         8         0         2         2
  9Q GAIN WILD-TYPE      28        8        30         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q GAIN CNV                3          2          2        3         0
  9Q GAIN WILD-TYPE          6         21         11       14         9
D18V11, multiclass

Clustering(19) Variable = 10p gain
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN CNV         5   1
  10P GAIN WILD-TYPE 114  10
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                124 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                 10 
$`10P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       17.03        13.02         1.02        12.00        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-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-4749 
        9.37         4.70        13.97        60.00         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        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-A1DG TCGA-DY-A1H8 
      119.51        41.33        57.24       121.08        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-F5-6811 
        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 

      10P GAIN CNV 10P GAIN WILD-TYPE 
              1.02               0.16 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             70.03             121.08 
      10P GAIN CNV 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 CNV" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          5    3
  10P GAIN WILD-TYPE   69   85
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  FEMALE            5                 69
  MALE              3                 85
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          8    0
  10P GAIN WILD-TYPE  135   13
                                clus
vv                               10P GAIN CNV 10P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     8                135
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D19V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          0    8
  10P GAIN WILD-TYPE    6  148
     clus
vv    10P GAIN CNV 10P GAIN WILD-TYPE
  NO             0                  6
  YES            8                148
                    vv
clus                  M0  M1 M1A  MX
  10P GAIN CNV         6   2   0   0
  10P GAIN WILD-TYPE 117  20   2  13
D19V6, multiclass
     clus
vv    10P GAIN CNV 10P GAIN WILD-TYPE
  M0             6                117
  M1             2                 20
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  10P GAIN CNV        4  0   1   0   0  3   0   0  0
  10P GAIN WILD-TYPE 79 35   3   5   1 20   2   7  1
D19V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  10P GAIN CNV         6   0   1   0
  10P GAIN WILD-TYPE 115   2  11   3
D19V8, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  R0            6                115
  R1            0                  2
  R2            1                 11
  RX            0                  3
D19V9, continuous
D19V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P GAIN CNV             1        1         2         0         0         0
  10P GAIN WILD-TYPE      29        7        36         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P GAIN CNV                0          1          1        2         0
  10P GAIN WILD-TYPE          9         22         12       15         9
D19V11, multiclass

Clustering(20) Variable = 10q gain
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN CNV         4   0
  10Q GAIN WILD-TYPE 115  11
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 4                126 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 0                 11 
$`10Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-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-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-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 

      10Q GAIN CNV 10Q GAIN WILD-TYPE 
              1.02               0.16 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
             70.03             121.08 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
            13.415              6.085 
[1] "1.0 - 70.0 (13.4)" "0.2 - 121.1 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"10Q GAIN WILD-TYPE"       "10Q GAIN CNV" "10Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"10Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          4    0
  10Q GAIN WILD-TYPE   70   88
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  FEMALE            4                 70
  MALE              0                 88
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          4    0
  10Q GAIN WILD-TYPE  139   13
                                clus
vv                               10Q GAIN CNV 10Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     4                139
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D20V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          0    4
  10Q GAIN WILD-TYPE    6  152
     clus
vv    10Q GAIN CNV 10Q GAIN WILD-TYPE
  NO             0                  6
  YES            4                152
                    vv
clus                  M0  M1 M1A  MX
  10Q GAIN CNV         3   1   0   0
  10Q GAIN WILD-TYPE 120  21   2  13
D20V6, multiclass
     clus
vv    10Q GAIN CNV 10Q GAIN WILD-TYPE
  M0             3                120
  M1             1                 21
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  10Q GAIN CNV        1  0   1   0   0  2   0   0  0
  10Q GAIN WILD-TYPE 82 35   3   5   1 21   2   7  1
D20V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN CNV         4   0   0   0
  10Q GAIN WILD-TYPE 117   2  12   3
D20V8, multiclass
    clus
vv   10Q GAIN CNV 10Q GAIN WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            0                 12
  RX            0                  3
D20V9, continuous
D20V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q GAIN CNV             0        1         0         0         0         0
  10Q GAIN WILD-TYPE      30        7        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q GAIN CNV                0          1          1        1         0
  10Q GAIN WILD-TYPE          9         22         12       16         9
D20V11, multiclass

Clustering(21) Variable = 11p gain
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN CNV        15   2
  11P GAIN WILD-TYPE 104   9
      11P GAIN CNV 11P GAIN WILD-TYPE 
                17                113 
      11P GAIN CNV 11P GAIN WILD-TYPE 
                 2                  9 
$`11P GAIN CNV`
TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-4007 TCGA-AG-A01N 
       10.39         6.35        12.00         1.02         1.02        12.00 
TCGA-AH-6897 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        4.60         9.37        11.01         5.03         8.98        27.91 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6885 TCGA-G5-6233 
       19.99       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-3586 TCGA-AG-3599 TCGA-AG-3605 
        1.02         1.02         2.01         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.96         0.95         1.02         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-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-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-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-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.02         6.94         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98         9.99         7.36         6.97         6.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.92         3.98         5.00         0.26        41.33        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      121.08        24.13        51.48        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-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-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-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        47.70        47.08        20.91 

      11P GAIN CNV 11P GAIN WILD-TYPE 
              1.02               0.16 
      11P GAIN CNV 11P GAIN WILD-TYPE 
            119.51             121.08 
      11P GAIN CNV 11P GAIN WILD-TYPE 
              9.37               6.02 
[1] "1.0 - 119.5 (9.4)" "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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11P GAIN CNV"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN 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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11P GAIN CNV"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN 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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "11P GAIN CNV" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11P GAIN CNV"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"       "11P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P GAIN WILD-TYPE"       "11P GAIN CNV" "11P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "11P GAIN CNV" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          7   14
  11P GAIN WILD-TYPE   67   74
        clus
vv       11P GAIN CNV 11P GAIN WILD-TYPE
  FEMALE            7                 67
  MALE             14                 74
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV         21    0
  11P GAIN WILD-TYPE  122   13
                                clus
vv                               11P GAIN CNV 11P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    21                122
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D21V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN CNV          0   21
  11P GAIN WILD-TYPE    6  135
     clus
vv    11P GAIN CNV 11P GAIN WILD-TYPE
  NO             0                  6
  YES           21                135
                    vv
clus                  M0  M1 M1A  MX
  11P GAIN CNV        16   5   0   0
  11P GAIN WILD-TYPE 107  17   2  13
D21V6, multiclass
     clus
vv    11P GAIN CNV 11P GAIN WILD-TYPE
  M0            16                107
  M1             5                 17
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  11P GAIN CNV       12  2   2   1   0  3   0   1  0
  11P GAIN WILD-TYPE 71 33   2   4   1 20   2   6  1
D21V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  11P GAIN CNV        17   0   2   0
  11P GAIN WILD-TYPE 104   2  10   3
D21V8, multiclass
    clus
vv   11P GAIN CNV 11P GAIN WILD-TYPE
  R0           17                104
  R1            0                  2
  R2            2                 10
  RX            0                  3
D21V9, continuous
D21V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P GAIN CNV             6        1         4         0         1         0
  11P GAIN WILD-TYPE      24        7        34         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P GAIN CNV                1          2          1        3         1
  11P GAIN WILD-TYPE          8         21         12       14         8
D21V11, multiclass

Clustering(22) Variable = 11q gain
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN CNV        14   1
  11Q GAIN WILD-TYPE 105  10
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                15                115 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
                 1                 10 
$`11Q GAIN CNV`
TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3883 TCGA-AG-4007 TCGA-AG-A01N TCGA-AH-6897 
       10.39        12.00         1.02         1.02        12.00         4.60 
TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        9.37         4.70        11.01         5.03         8.98        27.91 
TCGA-DY-A0XA TCGA-EI-6885 TCGA-F5-6812 
      119.51         5.23         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-3586 TCGA-AG-3587 
        7.33         1.02         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-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-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-6903 
       38.01         0.49         1.45         0.69         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
       10.19         6.02         6.02         6.94        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98         9.99         7.36         6.97         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-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-F5-6813 TCGA-F5-6814 
        0.85         2.17         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        47.70        47.08 
TCGA-G5-6641 
       20.91 

      11Q GAIN CNV 11Q GAIN WILD-TYPE 
              0.66               0.16 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
            119.51             121.08 
      11Q GAIN CNV 11Q GAIN WILD-TYPE 
              8.98               6.15 
[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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11Q GAIN CNV"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN 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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11Q GAIN CNV"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN 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 CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV"       "11Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "11Q GAIN CNV"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q GAIN WILD-TYPE"       "11Q GAIN CNV" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"       "11Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "11Q GAIN CNV" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"11Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          7   10
  11Q GAIN WILD-TYPE   67   78
        clus
vv       11Q GAIN CNV 11Q GAIN WILD-TYPE
  FEMALE            7                 67
  MALE             10                 78
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV         17    0
  11Q GAIN WILD-TYPE  126   13
                                clus
vv                               11Q GAIN CNV 11Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    17                126
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D22V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN CNV          0   17
  11Q GAIN WILD-TYPE    6  139
     clus
vv    11Q GAIN CNV 11Q GAIN WILD-TYPE
  NO             0                  6
  YES           17                139
                    vv
clus                  M0  M1 M1A  MX
  11Q GAIN CNV        12   5   0   0
  11Q GAIN WILD-TYPE 111  17   2  13
D22V6, multiclass
     clus
vv    11Q GAIN CNV 11Q GAIN WILD-TYPE
  M0            12                111
  M1             5                 17
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  11Q GAIN CNV       11  1   2   1   0  1   0   1  0
  11Q GAIN WILD-TYPE 72 34   2   4   1 22   2   6  1
D22V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN CNV        12   0   2   0
  11Q GAIN WILD-TYPE 109   2  10   3
D22V8, multiclass
    clus
vv   11Q GAIN CNV 11Q GAIN WILD-TYPE
  R0           12                109
  R1            0                  2
  R2            2                 10
  RX            0                  3
D22V9, continuous
D22V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q GAIN CNV             6        1         3         0         0         0
  11Q GAIN WILD-TYPE      24        7        35         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q GAIN CNV                0          2          0        3         1
  11Q GAIN WILD-TYPE          9         21         13       14         8
D22V11, multiclass

Clustering(23) Variable = 12p gain
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN CNV        18   3
  12P GAIN WILD-TYPE 101   8
      12P GAIN CNV 12P GAIN WILD-TYPE 
                21                109 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 3                  8 
$`12P GAIN CNV`
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3883 
       17.62         8.45         7.33         1.02         7.96         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N 
        0.92         1.02        15.91        13.02        38.93        61.94 
TCGA-CL-5917 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       60.00       119.51        32.58         0.16         0.46         0.66 
TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
        5.23         2.76        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-3575 
       12.72        10.39        14.50         7.59         6.35        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 
        1.02         1.02         2.01         1.02         0.99         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 
        0.95         1.02         0.99         0.99         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-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-A02X TCGA-AG-A032 
       10.98        51.98        49.94         1.94        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-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.97         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-A1DC TCGA-DY-A1DD 
        5.92         3.98         5.00         0.26        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-6513 TCGA-EI-6514 TCGA-EI-6881 
        2.17         8.22         3.98         6.90         7.10         6.15 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        3.55         3.98         2.73         7.79         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 

      12P GAIN CNV 12P GAIN WILD-TYPE 
              0.16               0.26 
      12P GAIN CNV 12P GAIN WILD-TYPE 
            119.51             121.08 
      12P GAIN CNV 12P GAIN WILD-TYPE 
              7.96               6.02 
[1] "0.2 - 119.5 (8.0)" "0.3 - 121.1 (6.0)"
        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 CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12P GAIN CNV" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV         13   15
  12P GAIN WILD-TYPE   61   73
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  FEMALE           13                 61
  MALE             15                 73
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV         25    2
  12P GAIN WILD-TYPE  118   11
                                clus
vv                               12P GAIN CNV 12P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    25                118
  RECTAL MUCINOUS ADENOCARCINOMA            2                 11
D23V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          2   26
  12P GAIN WILD-TYPE    4  130
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  NO             2                  4
  YES           26                130
                    vv
clus                  M0  M1 M1A  MX
  12P GAIN CNV        21   3   0   4
  12P GAIN WILD-TYPE 102  19   2   9
D23V6, multiclass
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  M0            21                102
  M1             3                 19
  M1A            0                  2
  MX             4                  9
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  12P GAIN CNV       16  4   0   1   0  6   0   1  0
  12P GAIN WILD-TYPE 67 31   4   4   1 17   2   6  1
D23V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  12P GAIN CNV        20   0   2   1
  12P GAIN WILD-TYPE 101   2  10   2
D23V8, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  R0           20                101
  R1            0                  2
  R2            2                 10
  RX            1                  2
D23V9, continuous
D23V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P GAIN CNV             7        2         6         0         1         0
  12P GAIN WILD-TYPE      23        6        32         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P GAIN CNV                1          2          4        4         1
  12P GAIN WILD-TYPE          8         21          9       13         8
D23V11, multiclass

Clustering(24) Variable = 12q gain
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN CNV        11   3
  12Q GAIN WILD-TYPE 108   8
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                14                116 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 3                  8 
$`12Q GAIN CNV`
TCGA-AF-5654 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N 
        8.45         1.02         1.02        13.02        38.93        61.94 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
      119.51        32.58         0.16         0.46         0.66         5.23 
TCGA-EI-7002 TCGA-G5-6233 
        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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-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-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-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-A02X TCGA-AG-A032 
       10.98        51.98        49.94         1.94        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-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-EF-5830 TCGA-EF-5831 
       57.24       121.08        24.13        51.48         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
        7.63         2.17         8.22         3.98         6.90         7.10 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 
        6.15         3.55         3.98         2.73         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-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.08         0.76         0.46        47.70 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        20.91 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              0.16               0.26 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
            119.51             121.08 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              6.84               6.25 
[1] "0.2 - 119.5 (6.8)" "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 CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12Q GAIN 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 CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"12Q GAIN 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 CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"12Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV         11    8
  12Q GAIN WILD-TYPE   63   80
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  FEMALE           11                 63
  MALE              8                 80
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV         17    1
  12Q GAIN WILD-TYPE  126   12
                                clus
vv                               12Q GAIN CNV 12Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    17                126
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D24V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          0   19
  12Q GAIN WILD-TYPE    6  137
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  NO             0                  6
  YES           19                137
                    vv
clus                  M0  M1 M1A  MX
  12Q GAIN CNV        15   3   0   1
  12Q GAIN WILD-TYPE 108  19   2  12
D24V6, multiclass
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0            15                108
  M1             3                 19
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  12Q GAIN CNV       11  4   0   1   0  3   0   0  0
  12Q GAIN WILD-TYPE 72 31   4   4   1 20   2   7  1
D24V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN CNV        14   0   2   0
  12Q GAIN WILD-TYPE 107   2  10   3
D24V8, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  R0           14                107
  R1            0                  2
  R2            2                 10
  RX            0                  3
D24V9, continuous
D24V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q GAIN CNV             4        2         4         0         1         0
  12Q GAIN WILD-TYPE      26        6        34         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q GAIN CNV                1          2          1        3         1
  12Q GAIN WILD-TYPE          8         21         12       14         8
D24V11, multiclass

Clustering(25) Variable = 13q gain
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN CNV       75 11
  13Q GAIN WILD-TYPE 44  0
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                86                 44 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                11                  0 
$`13Q GAIN CNV`
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-3586 TCGA-AG-3587 TCGA-AG-3727 TCGA-AG-3742 
        1.02         2.01         1.02         1.02         0.95         0.99 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        0.92         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 
        1.02         1.02         0.99         6.02        25.94        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
       13.02         1.02        12.00        63.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.93        38.01         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        4.60         6.02         6.94         9.37         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        10.98        11.01         5.03         8.98 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       27.91         6.97         5.00        41.33        57.24       121.08 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 
       24.13        51.48        32.58         0.49         7.63         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-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
        3.98         2.73         2.76         3.39         0.85         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 
        0.39         1.02         0.66         0.69         0.76        18.25 
TCGA-G5-6235 TCGA-G5-6572 
       47.70        47.08 

$`13Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3599 TCGA-AG-3605 
       19.53        12.72         8.45        12.00         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-A002 
        7.96         1.02         0.99         1.02         1.02        20.94 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       13.91        23.01        17.03         1.02        12.00        70.03 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 
       10.98        61.94        40.96         1.45         1.81        10.19 
TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
        6.02         9.99         7.36         6.97        19.99         5.92 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
        3.98         0.26       119.51         2.40         0.16         2.17 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 
        3.55         5.23         7.79         2.04         0.53         1.08 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        20.91 

      13Q GAIN CNV 13Q GAIN WILD-TYPE 
              0.39               0.16 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
            121.08             119.51 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
             6.250              6.495 
[1] "0.4 - 121.1 (6.2)" "0.2 - 119.5 (6.5)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-G5-6641 
"13Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-G5-6641 
"13Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "13Q GAIN CNV"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "13Q GAIN CNV"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-G5-6641 
"13Q GAIN WILD-TYPE" 
[1] "hr="     "3.4e+08"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV         46   56
  13Q GAIN WILD-TYPE   28   32
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  FEMALE           46                 28
  MALE             56                 32
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV         96    2
  13Q GAIN WILD-TYPE   47   11
                                clus
vv                               13Q GAIN CNV 13Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    96                 47
  RECTAL MUCINOUS ADENOCARCINOMA            2                 11
D25V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          3   99
  13Q GAIN WILD-TYPE    3   57
     clus
vv    13Q GAIN CNV 13Q GAIN WILD-TYPE
  NO             3                  3
  YES           99                 57
                    vv
clus                 M0 M1 M1A MX
  13Q GAIN CNV       76 15   0 10
  13Q GAIN WILD-TYPE 47  7   2  3
D25V6, multiclass
     clus
vv    13Q GAIN CNV 13Q GAIN WILD-TYPE
  M0            76                 47
  M1            15                  7
  M1A            0                  2
  MX            10                  3
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  13Q GAIN CNV       44 26   3   2   1 18   1   5  1
  13Q GAIN WILD-TYPE 39  9   1   3   0  5   1   2  0
D25V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN CNV       72  2  7  2
  13Q GAIN WILD-TYPE 49  0  5  1
D25V8, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  R0           72                 49
  R1            2                  0
  R2            7                  5
  RX            2                  1
D25V9, continuous
D25V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q GAIN CNV            17        3        20         2         2         3
  13Q GAIN WILD-TYPE      13        5        18         0         0         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q GAIN CNV                5         19         10       11         5
  13Q GAIN WILD-TYPE          4          4          3        6         4
D25V11, multiclass

Clustering(26) Variable = 14q gain
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN CNV         4   0
  14Q GAIN WILD-TYPE 115  11
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                126 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 0                 11 
$`14Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        10.98        51.98        49.94         1.94 
TCGA-AG-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-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-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-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 

      14Q GAIN CNV 14Q GAIN WILD-TYPE 
              0.66               0.16 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
             63.98             121.08 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
              6.41               6.25 
[1] "0.7 - 64.0 (6.4)"  "0.2 - 121.1 (6.2)"
        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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "14Q GAIN CNV" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"14Q GAIN WILD-TYPE" 
[1] "hr="     "7.7e+07"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          4    0
  14Q GAIN WILD-TYPE   70   88
        clus
vv       14Q GAIN CNV 14Q GAIN WILD-TYPE
  FEMALE            4                 70
  MALE              0                 88
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          4    0
  14Q GAIN WILD-TYPE  139   13
                                clus
vv                               14Q GAIN CNV 14Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     4                139
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D26V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          1    3
  14Q GAIN WILD-TYPE    5  153
     clus
vv    14Q GAIN CNV 14Q GAIN WILD-TYPE
  NO             1                  5
  YES            3                153
                    vv
clus                  M0  M1 M1A  MX
  14Q GAIN CNV         2   1   0   1
  14Q GAIN WILD-TYPE 121  21   2  12
D26V6, multiclass
     clus
vv    14Q GAIN CNV 14Q GAIN WILD-TYPE
  M0             2                121
  M1             1                 21
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  14Q GAIN CNV        1  1   0   2   0  0   0   0  0
  14Q GAIN WILD-TYPE 82 34   4   3   1 23   2   7  1
D26V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN CNV         3   0   0   0
  14Q GAIN WILD-TYPE 118   2  12   3
D26V8, multiclass
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  R0            3                118
  R1            0                  2
  R2            0                 12
  RX            0                  3
D26V9, continuous
D26V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q GAIN CNV             0        1         0         0         0         0
  14Q GAIN WILD-TYPE      30        7        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q GAIN CNV                0          2          0        1         0
  14Q GAIN WILD-TYPE          9         21         13       16         9
D26V11, multiclass

Clustering(27) Variable = 16p gain
D27V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV       23  0
  16P GAIN WILD-TYPE 96 11
      16P GAIN CNV 16P GAIN WILD-TYPE 
                23                107 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 0                 11 
$`16P GAIN CNV`
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         7.96         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-3575 TCGA-AG-3581 
       10.39        14.50         8.45         7.33        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        17.03         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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       40.96         0.49         1.45         0.69         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.02         6.02         9.37         4.70        13.97 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        7.99        10.98         9.99         5.03         7.36         6.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       27.91         6.97        19.99         5.92         3.98         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-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-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-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.85         1.02         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 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              0.39               0.16 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             60.00             121.08 
      16P GAIN CNV 16P GAIN WILD-TYPE 
              7.10               6.02 
[1] "0.4 - 60.0 (7.1)"  "0.2 - 121.1 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "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 CNV" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "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 CNV" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "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 CNV" "16P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16P GAIN WILD-TYPE" 
[1] "hr="     "2.2e+08"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV         15   14
  16P GAIN WILD-TYPE   59   74
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE           15                 59
  MALE             14                 74
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV         29    0
  16P GAIN WILD-TYPE  114   13
                                clus
vv                               16P GAIN CNV 16P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    29                114
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D27V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          2   27
  16P GAIN WILD-TYPE    4  129
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  NO             2                  4
  YES           27                129
                    vv
clus                  M0  M1 M1A  MX
  16P GAIN CNV        20   5   0   4
  16P GAIN WILD-TYPE 103  17   2   9
D27V6, multiclass
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  M0            20                103
  M1             5                 17
  M1A            0                  2
  MX             4                  9
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  16P GAIN CNV       12  8   0   2   0  5   0   1  1
  16P GAIN WILD-TYPE 71 27   4   3   1 18   2   6  0
D27V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  16P GAIN CNV        21   0   3   1
  16P GAIN WILD-TYPE 100   2   9   2
D27V8, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  R0           21                100
  R1            0                  2
  R2            3                  9
  RX            1                  2
D27V9, continuous
D27V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P GAIN CNV             4        1         5         1         0         1
  16P GAIN WILD-TYPE      26        7        33         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P GAIN CNV                1          8          2        3         2
  16P GAIN WILD-TYPE          8         15         11       14         7
D27V11, multiclass

Clustering(28) Variable = 16q gain
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN CNV       23  2
  16Q GAIN WILD-TYPE 96  9
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                25                105 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                  9 
$`16Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 
       14.50         8.45         7.33        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        17.03         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-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       40.96         0.49         1.45         0.69         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-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-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-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-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.85         1.02         0.53         1.08         0.46        18.25 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       47.70        47.08        20.91 

      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              0.39               0.16 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
             60.00             121.08 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              7.10               6.02 
[1] "0.4 - 60.0 (7.1)"  "0.2 - 121.1 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "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 CNV"       "16Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "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 CNV"       "16Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "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 CNV"       "16Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"16Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV         14   16
  16Q GAIN WILD-TYPE   60   72
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  FEMALE           14                 60
  MALE             16                 72
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV         30    0
  16Q GAIN WILD-TYPE  113   13
                                clus
vv                               16Q GAIN CNV 16Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    30                113
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D28V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          2   28
  16Q GAIN WILD-TYPE    4  128
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  NO             2                  4
  YES           28                128
                    vv
clus                  M0  M1 M1A  MX
  16Q GAIN CNV        19   7   0   4
  16Q GAIN WILD-TYPE 104  15   2   9
D28V6, multiclass
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  M0            19                104
  M1             7                 15
  M1A            0                  2
  MX             4                  9
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  16Q GAIN CNV       11  8   1   2   0  6   0   1  1
  16Q GAIN WILD-TYPE 72 27   3   3   1 17   2   6  0
D28V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN CNV       23  0  2  1
  16Q GAIN WILD-TYPE 98  2 10  2
D28V8, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  R0           23                 98
  R1            0                  2
  R2            2                 10
  RX            1                  2
D28V9, continuous
D28V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q GAIN CNV             3        1         6         0         0         1
  16Q GAIN WILD-TYPE      27        7        32         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q GAIN CNV                1          7          3        3         3
  16Q GAIN WILD-TYPE          8         16         10       14         6
D28V11, multiclass

Clustering(29) Variable = 17p gain
D29V1, survival
                    sevent
clus2                  0   1
  17P GAIN CNV         2   0
  17P GAIN WILD-TYPE 117  11
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                128 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 0                 11 
$`17P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-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-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 

      17P GAIN CNV 17P GAIN WILD-TYPE 
              8.98               0.16 
      17P GAIN CNV 17P GAIN WILD-TYPE 
              9.37             121.08 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             9.175              6.085 
[1] "9.0 - 9.4 (9.2)"   "0.2 - 121.1 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN 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-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN 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-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                128 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6624         TCGA-CL-4957 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-4745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        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" 
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          2    1
  17P GAIN WILD-TYPE   72   87
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  FEMALE            2                 72
  MALE              1                 87
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          3    0
  17P GAIN WILD-TYPE  140   13
                                clus
vv                               17P GAIN CNV 17P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     3                140
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D29V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          0    3
  17P GAIN WILD-TYPE    6  153
     clus
vv    17P GAIN CNV 17P GAIN WILD-TYPE
  NO             0                  6
  YES            3                153
                    vv
clus                  M0  M1 M1A  MX
  17P GAIN CNV         2   1   0   0
  17P GAIN WILD-TYPE 121  21   2  13
D29V6, multiclass
     clus
vv    17P GAIN CNV 17P GAIN WILD-TYPE
  M0             2                121
  M1             1                 21
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  17P GAIN CNV        1  0   0   0   0  1   0   1  0
  17P GAIN WILD-TYPE 82 35   4   5   1 22   2   6  1
D29V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  17P GAIN CNV         2   0   0   0
  17P GAIN WILD-TYPE 119   2  12   3
D29V8, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                136 
        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-3400 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AG-3574         TCGA-AG-3575 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3591 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3592         TCGA-AG-3593         TCGA-AG-3594 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3611         TCGA-AG-3612 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3725         TCGA-AG-3726         TCGA-AG-3727 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3728         TCGA-AG-3731         TCGA-AG-3732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3882 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3902         TCGA-AG-3909 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4021         TCGA-AG-4022         TCGA-AG-A002 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6897         TCGA-AH-6903 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BM-6198         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-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-F5-6464 
"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-F5-6812         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-G5-6641 
"17P GAIN WILD-TYPE" 
D29V9, continuous
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                150 
        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-3574 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3591         TCGA-AG-3592         TCGA-AG-3593 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3611 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3725         TCGA-AG-3726 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3731 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-3878 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-4021 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A002         TCGA-AG-A008 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A025 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032         TCGA-AH-6544 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AH-6897         TCGA-AH-6903         TCGA-BM-6198 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CL-4957         TCGA-DC-4745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        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-DY-A0XA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-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-F5-6464 
"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" 
D29V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P GAIN CNV             1        0         0         0         0         0
  17P GAIN WILD-TYPE      29        8        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P GAIN CNV                0          0          1        0         1
  17P GAIN WILD-TYPE          9         23         12       17         8
D29V11, multiclass

Clustering(30) Variable = 17q gain
D30V1, survival
                    sevent
clus2                  0   1
  17Q GAIN CNV        14   0
  17Q GAIN WILD-TYPE 105  11
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                14                116 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 0                 11 
$`17Q GAIN CNV`
TCGA-AF-2690 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N 
       11.77        12.00         1.02        15.91         1.02        12.00 
TCGA-AH-6897 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-EI-6509 TCGA-EI-6514 
        4.60         8.98         3.98         5.00         8.22         7.10 
TCGA-EI-7002 TCGA-F5-6811 
        2.76         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-3586 TCGA-AG-3599 
        7.33         1.02         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-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-A015 
       13.91         6.02        25.94        23.01        17.03        13.02 
TCGA-AG-A01J TCGA-AG-A01L 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-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-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-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-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
        2.17         0.46         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-F5-6812 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 

      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              1.02               0.16 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             15.91             121.08 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              6.05               6.25 
[1] "1.0 - 15.9 (6.0)"  "0.2 - 121.1 (6.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"17Q GAIN WILD-TYPE" 
[1] "hr="     "2.9e+07"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          7   11
  17Q GAIN WILD-TYPE   67   77
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  FEMALE            7                 67
  MALE             11                 77
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV         18    0
  17Q GAIN WILD-TYPE  125   13
                                clus
vv                               17Q GAIN CNV 17Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    18                125
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D30V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          0   18
  17Q GAIN WILD-TYPE    6  138
     clus
vv    17Q GAIN CNV 17Q GAIN WILD-TYPE
  NO             0                  6
  YES           18                138
                    vv
clus                  M0  M1 M1A  MX
  17Q GAIN CNV        14   4   0   0
  17Q GAIN WILD-TYPE 109  18   2  13
D30V6, multiclass
     clus
vv    17Q GAIN CNV 17Q GAIN WILD-TYPE
  M0            14                109
  M1             4                 18
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  17Q GAIN CNV       10  1   0   1   0  4   0   2  0
  17Q GAIN WILD-TYPE 73 34   4   4   1 19   2   5  1
D30V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN CNV        14   0   3   0
  17Q GAIN WILD-TYPE 107   2   9   3
D30V8, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  R0           14                107
  R1            0                  2
  R2            3                  9
  RX            0                  3
D30V9, continuous
D30V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q GAIN CNV             3        1         5         0         0         0
  17Q GAIN WILD-TYPE      27        7        33         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q GAIN CNV                0          2          2        3         1
  17Q GAIN WILD-TYPE          9         21         11       14         8
D30V11, multiclass

Clustering(31) Variable = 18p gain
D31V1, survival
                    sevent
clus2                  0   1
  18P GAIN CNV         2   1
  18P GAIN WILD-TYPE 117  10
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                127 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 10 
$`18P GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        6.35        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        10.98        51.98        49.94         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01         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 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              7.33               0.16 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             63.98             121.08 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             38.93               6.02 
[1] "7.3 - 64.0 (38.9)" "0.2 - 121.1 (6.0)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          3    4
  18P GAIN WILD-TYPE   71   84
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            3                 71
  MALE              4                 84
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          6    1
  18P GAIN WILD-TYPE  137   12
                                clus
vv                               18P GAIN CNV 18P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     6                137
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D31V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    6
  18P GAIN WILD-TYPE    5  150
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  NO             1                  5
  YES            6                150
                    vv
clus                  M0  M1 M1A  MX
  18P GAIN CNV         4   1   0   2
  18P GAIN WILD-TYPE 119  21   2  11
D31V6, multiclass
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  M0             4                119
  M1             1                 21
  M1A            0                  2
  MX             2                 11
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  18P GAIN CNV        2  2   0   0   0  1   1   1  0
  18P GAIN WILD-TYPE 81 33   4   5   1 22   1   6  1
D31V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  18P GAIN CNV         4   0   1   0
  18P GAIN WILD-TYPE 117   2  11   3
D31V8, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            1                 11
  RX            0                  3
D31V9, continuous
D31V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P GAIN CNV             0        1         1         0         0         1
  18P GAIN WILD-TYPE      30        7        37         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P GAIN CNV                0          0          2        2         0
  18P GAIN WILD-TYPE          9         23         11       15         9
D31V11, multiclass

Clustering(32) Variable = 18q gain
D32V1, survival
                    sevent
clus2                  0   1
  18Q GAIN CNV         1   1
  18Q GAIN WILD-TYPE 118  10
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                128 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 10 
$`18Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        6.35        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.94        40.96        38.01         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.02         6.94         9.37         4.70        13.97        60.00 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01         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 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              7.33               0.16 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             38.93             121.08 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
            23.130              6.085 
[1] "7.3 - 38.9 (23.1)" "0.2 - 121.1 (6.1)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"18Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                128 
        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-3575         TCGA-AG-3581 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3586 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3587         TCGA-AG-3599         TCGA-AG-3605 
"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-3883 
"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-3896         TCGA-AG-3999 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4022         TCGA-AG-A002         TCGA-AG-A008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01J         TCGA-AG-A01L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A01N         TCGA-AG-A01W         TCGA-AG-A01Y 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A023         TCGA-AG-A025 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02N         TCGA-AG-A02X 
"18Q GAIN WILD-TYPE" "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" 
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    3
  18Q GAIN WILD-TYPE   73   85
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            1                 73
  MALE              3                 85
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          4    0
  18Q GAIN WILD-TYPE  139   13
                                clus
vv                               18Q GAIN CNV 18Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     4                139
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D32V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    3
  18Q GAIN WILD-TYPE    5  153
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  NO             1                  5
  YES            3                153
                    vv
clus                  M0  M1 M1A  MX
  18Q GAIN CNV         1   1   0   2
  18Q GAIN WILD-TYPE 122  21   2  11
D32V6, multiclass
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0             1                122
  M1             1                 21
  M1A            0                  2
  MX             2                 11
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  18Q GAIN CNV        0  2   0   0   0  0   1   1  0
  18Q GAIN WILD-TYPE 83 33   4   5   1 23   1   6  1
D32V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN CNV         1   0   1   0
  18Q GAIN WILD-TYPE 120   2  11   3
D32V8, multiclass
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                136 
        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-3400 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AG-3574         TCGA-AG-3575 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3591 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3592         TCGA-AG-3593         TCGA-AG-3594 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3725         TCGA-AG-3726 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3728         TCGA-AG-3731 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-3878 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-4021         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-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6897         TCGA-AH-6903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CL-5917         TCGA-CL-5918 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-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-F5-6812         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-G5-6641 
"18Q GAIN WILD-TYPE" 
D32V9, continuous
D32V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q GAIN CNV             0        0         0         0         0         1
  18Q GAIN WILD-TYPE      30        8        38         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q GAIN CNV                0          0          1        2         0
  18Q GAIN WILD-TYPE          9         23         12       15         9
D32V11, multiclass

Clustering(33) Variable = 19p gain
D33V1, survival
                    sevent
clus2                  0   1
  19P GAIN CNV        15   1
  19P GAIN WILD-TYPE 104  10
      19P GAIN CNV 19P GAIN WILD-TYPE 
                16                114 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 1                 10 
$`19P GAIN CNV`
TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A014 
       11.77         1.02         1.02         1.02         1.02        15.91 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 
       12.00         1.94        38.01        10.98        11.01         8.98 
TCGA-DY-A1DE TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 
      121.08         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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 
        7.33        12.00         1.02         2.01         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         1.02         0.99        20.94        13.91         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.94        23.01        17.03        13.02         1.02         1.02 
TCGA-AG-A01L 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-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        40.96         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-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 

      19P GAIN CNV 19P GAIN WILD-TYPE 
              0.66               0.16 
      19P GAIN CNV 19P GAIN WILD-TYPE 
            121.08             119.51 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             8.040              6.085 
[1] "0.7 - 121.1 (8.0)" "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 CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19P GAIN CNV"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19P GAIN CNV"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19P GAIN CNV"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV         11    9
  19P GAIN WILD-TYPE   63   79
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  FEMALE           11                 63
  MALE              9                 79
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV         20    0
  19P GAIN WILD-TYPE  123   13
                                clus
vv                               19P GAIN CNV 19P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    20                123
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D33V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          0   20
  19P GAIN WILD-TYPE    6  136
     clus
vv    19P GAIN CNV 19P GAIN WILD-TYPE
  NO             0                  6
  YES           20                136
                    vv
clus                  M0  M1 M1A  MX
  19P GAIN CNV        15   5   0   0
  19P GAIN WILD-TYPE 108  17   2  13
D33V6, multiclass
     clus
vv    19P GAIN CNV 19P GAIN WILD-TYPE
  M0            15                108
  M1             5                 17
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  19P GAIN CNV       10  3   1   1   0  4   0   1  0
  19P GAIN WILD-TYPE 73 32   3   4   1 19   2   6  1
D33V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  19P GAIN CNV        15   1   3   0
  19P GAIN WILD-TYPE 106   1   9   3
D33V8, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  R0           15                106
  R1            1                  1
  R2            3                  9
  RX            0                  3
D33V9, continuous
D33V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P GAIN CNV             5        1         3         0         0         0
  19P GAIN WILD-TYPE      25        7        35         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P GAIN CNV                0          3          2        4         1
  19P GAIN WILD-TYPE          9         20         11       13         8
D33V11, multiclass

Clustering(34) Variable = 19q gain
D34V1, survival
                    sevent
clus2                  0   1
  19Q GAIN CNV        17   1
  19Q GAIN WILD-TYPE 102  10
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                18                112 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                 10 
$`19Q GAIN CNV`
TCGA-AG-3587 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        1.02         1.02         1.02        15.91        13.02         1.02 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CL-4957 TCGA-DC-4745 
       12.00         1.94        38.01         6.02        13.97        10.98 
TCGA-DC-4749 TCGA-DC-6154 TCGA-DY-A1DE TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 
       11.01         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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-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-A01J 
       13.91         6.02        25.94        23.01        17.03         1.02 
TCGA-AG-A01L 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-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        40.96         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        9.37         4.70        60.00         7.99         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-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-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-6513 
        0.16         2.17         8.22         0.46         3.98         6.90 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
        6.15         3.55         3.98         2.73         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 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              0.66               0.16 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
            121.08             119.51 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             8.040              6.085 
[1] "0.7 - 121.1 (8.0)" "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-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE" "19Q GAIN 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-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q GAIN WILD-TYPE" "19Q GAIN 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-3575 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "19Q GAIN CNV"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV         13   10
  19Q GAIN WILD-TYPE   61   78
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  FEMALE           13                 61
  MALE             10                 78
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV         23    0
  19Q GAIN WILD-TYPE  120   13
                                clus
vv                               19Q GAIN CNV 19Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    23                120
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D34V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          0   23
  19Q GAIN WILD-TYPE    6  133
     clus
vv    19Q GAIN CNV 19Q GAIN WILD-TYPE
  NO             0                  6
  YES           23                133
                    vv
clus                  M0  M1 M1A  MX
  19Q GAIN CNV        17   6   0   0
  19Q GAIN WILD-TYPE 106  16   2  13
D34V6, multiclass
     clus
vv    19Q GAIN CNV 19Q GAIN WILD-TYPE
  M0            17                106
  M1             6                 16
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  19Q GAIN CNV       12  4   1   1   1  3   0   1  0
  19Q GAIN WILD-TYPE 71 31   3   4   0 20   2   6  1
D34V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN CNV        15   1   4   0
  19Q GAIN WILD-TYPE 106   1   8   3
D34V8, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  R0           15                106
  R1            1                  1
  R2            4                  8
  RX            0                  3
D34V9, continuous
D34V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q GAIN CNV             6        1         4         0         0         0
  19Q GAIN WILD-TYPE      24        7        34         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q GAIN CNV                1          4          1        5         1
  19Q GAIN WILD-TYPE          8         19         12       12         8
D34V11, multiclass

Clustering(35) Variable = 20p gain
D35V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV       73  5
  20P GAIN WILD-TYPE 46  6
      20P GAIN CNV 20P GAIN WILD-TYPE 
                78                 52 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 5                  6 
$`20P GAIN CNV`
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-3586 
        8.45         6.35         7.33         1.02         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        1.02         0.99         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.92         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02         1.02         6.02        25.94        23.01        17.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       13.02         1.02        51.98        40.96        38.01         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37         4.70        13.97        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-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6506 
        5.92       119.51       121.08        24.13         2.40         7.63 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
        2.17         8.22         0.46         3.98         0.66         7.10 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
        3.98         5.23         2.76         3.39         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.66         1.08         0.76        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-3575 
       10.62        13.55        12.72        14.50         7.59        12.00 
TCGA-AG-3583 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-4022 
        2.01         0.99         7.96         1.02         0.99         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       20.94        13.91        15.91         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        63.98        10.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 
       61.94         1.45        10.19         6.02        60.00         7.99 
TCGA-DC-4749 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       11.01         3.98         5.00         0.26        41.33        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6881 
       51.48        32.58         0.49         0.16         6.90         6.15 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
        3.55         2.73         7.79         2.04         0.85         2.17 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6864 TCGA-G5-6641 
        0.69         0.53         0.46        20.91 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.39               0.16 
      20P GAIN CNV 20P GAIN WILD-TYPE 
            121.08              70.03 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             5.575              7.875 
[1] "0.4 - 121.1 (5.6)" "0.2 - 70.0 (7.9)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20P GAIN CNV"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-G5-6641 
"20P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV         39   56
  20P GAIN WILD-TYPE   35   32
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE           39                 35
  MALE             56                 32
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV         90    2
  20P GAIN WILD-TYPE   53   11
                                clus
vv                               20P GAIN CNV 20P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    90                 53
  RECTAL MUCINOUS ADENOCARCINOMA            2                 11
D35V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          3   92
  20P GAIN WILD-TYPE    3   64
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  NO             3                  3
  YES           92                 64
                    vv
clus                 M0 M1 M1A MX
  20P GAIN CNV       71 14   2  7
  20P GAIN WILD-TYPE 52  8   0  6
D35V6, multiclass
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  M0            71                 52
  M1            14                  8
  M1A            2                  0
  MX             7                  6
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  20P GAIN CNV       46 16   4   3   1 16   2   5  1
  20P GAIN WILD-TYPE 37 19   0   2   0  7   0   2  0
D35V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  20P GAIN CNV       72  1  6  0
  20P GAIN WILD-TYPE 49  1  6  3
D35V8, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  R0           72                 49
  R1            1                  1
  R2            6                  6
  RX            0                  3
D35V9, continuous
D35V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P GAIN CNV            20        0        22         1         2         4
  20P GAIN WILD-TYPE      10        8        16         1         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P GAIN CNV                4         13          8       12         4
  20P GAIN WILD-TYPE          5         10          5        5         5
D35V11, multiclass

Clustering(36) Variable = 20q gain
D36V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV       98 11
  20Q GAIN WILD-TYPE 21  0
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
               109                 21 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                11                  0 
$`20Q GAIN CNV`
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-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        1.02         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02         1.02         0.99         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-A026 
       12.00        12.00        70.03        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.93        40.96        38.01         0.49         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-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.70        13.97         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-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-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-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        7.63         2.17         8.22         0.46         3.98         0.66 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
        6.90         7.10         3.98         2.73         5.23         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-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         1.08         0.76         0.46        18.25        47.70 
TCGA-G5-6572 
       47.08 

$`20Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 
       13.55        12.72        12.00         1.02        20.94        13.91 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-BM-6198 TCGA-CL-5917 
       63.98        49.94        61.94         1.45        10.19        60.00 
TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
        3.98         0.26         0.16         6.15         3.55         7.79 
TCGA-EI-7004 TCGA-F5-6814 TCGA-G5-6641 
        2.04         0.53        20.91 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.39               0.16 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
            121.08              63.98 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              6.02              10.19 
[1] "0.4 - 121.1 (6.0)" "0.2 - 64.0 (10.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6641 
"20Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6641 
"20Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-G5-6641 
"20Q GAIN WILD-TYPE" 
[1] "hr="     "3.3e+08"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV         59   73
  20Q GAIN WILD-TYPE   15   15
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE           59                 15
  MALE             73                 15
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV        124    4
  20Q GAIN WILD-TYPE   19    9
                                clus
vv                               20Q GAIN CNV 20Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                   124                 19
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D36V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          4  128
  20Q GAIN WILD-TYPE    2   28
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  NO             4                  2
  YES          128                 28
                    vv
clus                 M0 M1 M1A MX
  20Q GAIN CNV       98 21   2 10
  20Q GAIN WILD-TYPE 25  1   0  3
D36V6, multiclass
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  M0            98                 25
  M1            21                  1
  M1A            2                  0
  MX            10                  3
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  20Q GAIN CNV       63 30   4   5   1 19   2   6  1
  20Q GAIN WILD-TYPE 20  5   0   0   0  4   0   1  0
D36V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN CNV       96  2 11  1
  20Q GAIN WILD-TYPE 25  0  1  2
D36V8, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  R0           96                 25
  R1            2                  0
  R2           11                  1
  RX            1                  2
D36V9, continuous
D36V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20Q GAIN CNV            25        4        28         2         2         5
  20Q GAIN WILD-TYPE       5        4        10         0         0         0
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20Q GAIN CNV                6         21         10       16         8
  20Q GAIN WILD-TYPE          3          2          3        1         1
D36V11, multiclass

Clustering(37) Variable = 21q gain
D37V1, survival
                    sevent
clus2                  0   1
  21Q GAIN CNV         3   0
  21Q GAIN WILD-TYPE 116  11
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                127 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 0                 11 
$`21Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-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-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 

      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              0.72               0.16 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
             17.03             121.08 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              5.23               6.35 
[1] "0.7 - 17.0 (5.2)"  "0.2 - 121.1 (6.3)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"21Q GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          4    3
  21Q GAIN WILD-TYPE   70   85
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  FEMALE            4                 70
  MALE              3                 85
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          7    0
  21Q GAIN WILD-TYPE  136   13
                                clus
vv                               21Q GAIN CNV 21Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     7                136
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D37V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          0    7
  21Q GAIN WILD-TYPE    6  149
     clus
vv    21Q GAIN CNV 21Q GAIN WILD-TYPE
  NO             0                  6
  YES            7                149
                    vv
clus                  M0  M1 M1A  MX
  21Q GAIN CNV         4   2   0   1
  21Q GAIN WILD-TYPE 119  20   2  12
D37V6, multiclass
     clus
vv    21Q GAIN CNV 21Q GAIN WILD-TYPE
  M0             4                119
  M1             2                 20
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  21Q GAIN CNV        3  1   0   1   0  1   0   0  1
  21Q GAIN WILD-TYPE 80 34   4   4   1 22   2   7  0
D37V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN CNV         5   0   1   0
  21Q GAIN WILD-TYPE 116   2  11   3
D37V8, multiclass
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  R0            5                116
  R1            0                  2
  R2            1                 11
  RX            0                  3
D37V9, continuous
D37V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q GAIN CNV             1        0         2         0         0         0
  21Q GAIN WILD-TYPE      29        8        36         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q GAIN CNV                0          1          0        2         0
  21Q GAIN WILD-TYPE          9         22         13       15         9
D37V11, multiclass

Clustering(38) Variable = 22q gain
D38V1, survival
                    sevent
clus2                  0   1
  22Q GAIN CNV         2   1
  22Q GAIN WILD-TYPE 117  10
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                127 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                 10 
$`22Q GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         0.72         1.81        10.19         6.02 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-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-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-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 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              1.02               0.16 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             24.13             121.08 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              4.60               6.35 
[1] "1.0 - 24.1 (4.6)"  "0.2 - 121.1 (6.3)"
        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-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN 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-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN 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-3575 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G5-6641 
"22Q GAIN WILD-TYPE" 
[1] "hr=" "10" 
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          3    2
  22Q GAIN WILD-TYPE   71   86
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  FEMALE            3                 71
  MALE              2                 86
D38V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          5    0
  22Q GAIN WILD-TYPE  138   13
                                clus
vv                               22Q GAIN CNV 22Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                     5                138
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D38V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          0    5
  22Q GAIN WILD-TYPE    6  151
     clus
vv    22Q GAIN CNV 22Q GAIN WILD-TYPE
  NO             0                  6
  YES            5                151
                    vv
clus                  M0  M1 M1A  MX
  22Q GAIN CNV         4   1   0   0
  22Q GAIN WILD-TYPE 119  21   2  13
D38V6, multiclass
     clus
vv    22Q GAIN CNV 22Q GAIN WILD-TYPE
  M0             4                119
  M1             1                 21
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  22Q GAIN CNV        1  2   0   0   0  2   0   0  0
  22Q GAIN WILD-TYPE 82 33   4   5   1 21   2   7  1
D38V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN CNV         3   0   1   0
  22Q GAIN WILD-TYPE 118   2  11   3
D38V8, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  R0            3                118
  R1            0                  2
  R2            1                 11
  RX            0                  3
D38V9, continuous
D38V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q GAIN CNV             1        0         0         0         0         0
  22Q GAIN WILD-TYPE      29        8        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q GAIN CNV                0          1          2        1         0
  22Q GAIN WILD-TYPE          9         22         11       16         9
D38V11, multiclass

Clustering(39) Variable = Xq gain
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN CNV         6   0
  XQ GAIN WILD-TYPE 113  11
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                6               124 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                0                11 
$`XQ GAIN CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-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-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       17.03        15.91         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-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-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-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-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-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-F5-6571 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-F5-6863 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 

      XQ GAIN CNV XQ GAIN WILD-TYPE 
             0.46              0.16 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            13.02            121.08 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            2.205             6.625 
[1] "0.5 - 13.0 (2.2)"  "0.2 - 121.1 (6.6)"
       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-3575        TCGA-AG-3581 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ GAIN 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-3575        TCGA-AG-3581 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ GAIN 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-3575        TCGA-AG-3581 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "hr="     "3400000"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          3    4
  XQ GAIN WILD-TYPE   71   84
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  FEMALE           3                71
  MALE             4                84
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          6    1
  XQ GAIN WILD-TYPE  137   12
                                clus
vv                               XQ GAIN CNV XQ GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                    6               137
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D39V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          0    7
  XQ GAIN WILD-TYPE    6  149
     clus
vv    XQ GAIN CNV XQ GAIN WILD-TYPE
  NO            0                 6
  YES           7               149
                   vv
clus                 M0  M1 M1A  MX
  XQ GAIN CNV         4   2   0   1
  XQ GAIN WILD-TYPE 119  20   2  12
D39V6, multiclass
     clus
vv    XQ GAIN CNV XQ GAIN WILD-TYPE
  M0            4               119
  M1            2                20
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  XQ GAIN CNV        5  0   0   0   0  2   0   0  0
  XQ GAIN WILD-TYPE 78 35   4   5   1 21   2   7  1
D39V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN CNV         4   0   2   0
  XQ GAIN WILD-TYPE 117   2  10   3
D39V8, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  R0           4               117
  R1           0                 2
  R2           2                10
  RX           0                 3
D39V9, continuous
D39V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ GAIN CNV             2        0         2         0         0         0
  XQ GAIN WILD-TYPE      28        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ GAIN CNV                0          0          0        2         1
  XQ GAIN WILD-TYPE          9         23         13       15         8
D39V11, multiclass

Clustering(40) Variable = 1p loss
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS CNV        13   2
  1P LOSS WILD-TYPE 106   9
      1P LOSS CNV 1P LOSS WILD-TYPE 
               15               115 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2                 9 
$`1P LOSS CNV`
TCGA-AG-3883 TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02G TCGA-AH-6643 TCGA-BM-6198 
        1.02        23.01        12.00        38.93         0.69        10.19 
TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EI-6511 
        9.37        11.01         5.03        19.99       119.51         3.98 
TCGA-EI-7002 TCGA-F5-6811 TCGA-G5-6572 
        2.76         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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        0.99        20.94        13.91         6.02        25.94        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-A02N 
       63.98        10.98        51.98        49.94         1.94        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       40.96        38.01         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.02         6.02         6.94         4.70        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       60.00         7.99        10.98         9.99         8.98         7.36 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        6.97        27.91         6.97         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-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-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
        8.22         0.46         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-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-F5-6812 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-G5-6641 
       20.91 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.69              0.16 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           119.51            121.08 
      1P LOSS CNV 1P LOSS WILD-TYPE 
            10.19              6.02 
[1] "0.7 - 119.5 (10.2)" "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-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "1P LOSS CNV" "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-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "1P LOSS CNV" "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-3575        TCGA-AG-3581 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          6   15
  1P LOSS WILD-TYPE   68   73
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           6                68
  MALE            15                73
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV         20    0
  1P LOSS WILD-TYPE  123   13
                                clus
vv                               1P LOSS CNV 1P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   20               123
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D40V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          1   20
  1P LOSS WILD-TYPE    5  136
     clus
vv    1P LOSS CNV 1P LOSS WILD-TYPE
  NO            1                 5
  YES          20               136
                   vv
clus                 M0  M1 M1A  MX
  1P LOSS CNV        15   3   0   1
  1P LOSS WILD-TYPE 108  19   2  12
D40V6, multiclass
     clus
vv    1P LOSS CNV 1P LOSS WILD-TYPE
  M0           15               108
  M1            3                19
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  1P LOSS CNV        9  7   1   0   0  2   0   1  0
  1P LOSS WILD-TYPE 74 28   3   5   1 21   2   6  1
D40V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  1P LOSS CNV        13   0   2   0
  1P LOSS WILD-TYPE 108   2  10   3
D40V8, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  R0          13               108
  R1           0                 2
  R2           2                10
  RX           0                 3
D40V9, continuous
D40V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P LOSS CNV             5        0         4         0         0         1
  1P LOSS WILD-TYPE      25        8        34         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P LOSS CNV                0          6          1        3         0
  1P LOSS WILD-TYPE          9         17         12       14         9
D40V11, multiclass

Clustering(41) Variable = 1q loss
D41V1, survival
                   sevent
clus2                 0   1
  1Q LOSS CNV         5   0
  1Q LOSS WILD-TYPE 114  11
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5               125 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                0                11 
$`1Q LOSS CNV`
TCGA-AG-3883 TCGA-AG-A01L TCGA-BM-6198 TCGA-DC-5869 TCGA-EI-6511 
        1.02        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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       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-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60         1.81         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01         9.99         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-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-6512 TCGA-EI-6513 TCGA-EI-6514 
        2.17         8.22         0.46         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 

      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             1.02              0.16 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
            12.00            121.08 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             5.03              6.35 
[1] "1.0 - 12.0 (5.0)"  "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-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q LOSS WILD-TYPE" "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-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q LOSS WILD-TYPE" "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-3575        TCGA-AG-3581 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr="     "9400000"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    5
  1Q LOSS WILD-TYPE   72   83
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  FEMALE           2                72
  MALE             5                83
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          7    0
  1Q LOSS WILD-TYPE  136   13
                                clus
vv                               1Q LOSS CNV 1Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    7               136
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D41V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          1    6
  1Q LOSS WILD-TYPE    5  150
     clus
vv    1Q LOSS CNV 1Q LOSS WILD-TYPE
  NO            1                 5
  YES           6               150
                   vv
clus                 M0  M1 M1A  MX
  1Q LOSS CNV         5   1   0   0
  1Q LOSS WILD-TYPE 118  21   2  13
D41V6, multiclass
     clus
vv    1Q LOSS CNV 1Q LOSS WILD-TYPE
  M0            5               118
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  1Q LOSS CNV        1  4   1   0   0  1   0   0  0
  1Q LOSS WILD-TYPE 82 31   3   5   1 22   2   7  1
D41V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS CNV         6   0   1   0
  1Q LOSS WILD-TYPE 115   2  11   3
D41V8, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  R0           6               115
  R1           0                 2
  R2           1                11
  RX           0                 3
D41V9, continuous
D41V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q LOSS CNV             1        0         0         0         0         0
  1Q LOSS WILD-TYPE      29        8        38         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q LOSS CNV                0          5          0        1         0
  1Q LOSS WILD-TYPE          9         18         13       16         9
D41V11, multiclass

Clustering(42) Variable = 2p loss
D42V1, survival
                   sevent
clus2                 0   1
  2P LOSS CNV         3   0
  2P LOSS WILD-TYPE 116  11
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3               127 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                0                11 
$`2P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-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-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01         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 

      2P LOSS CNV 2P LOSS WILD-TYPE 
             1.02              0.16 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            40.96            121.08 
      2P LOSS CNV 2P LOSS WILD-TYPE 
             1.02              6.35 
[1] "1.0 - 41.0 (1.0)"  "0.2 - 121.1 (6.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+07"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          3    2
  2P LOSS WILD-TYPE   71   86
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  FEMALE           3                71
  MALE             2                86
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          3    1
  2P LOSS WILD-TYPE  140   12
                                clus
vv                               2P LOSS CNV 2P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    3               140
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D42V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          0    5
  2P LOSS WILD-TYPE    6  151
     clus
vv    2P LOSS CNV 2P LOSS WILD-TYPE
  NO            0                 6
  YES           5               151
                   vv
clus                 M0  M1 M1A  MX
  2P LOSS CNV         4   1   0   0
  2P LOSS WILD-TYPE 119  21   2  13
D42V6, multiclass
     clus
vv    2P LOSS CNV 2P LOSS WILD-TYPE
  M0            4               119
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  2P LOSS CNV        3  1   0   0   0  1   0   0  0
  2P LOSS WILD-TYPE 80 34   4   5   1 22   2   7  1
D42V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  2P LOSS CNV         3   0   1   0
  2P LOSS WILD-TYPE 118   2  11   3
D42V8, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  R0           3               118
  R1           0                 2
  R2           1                11
  RX           0                 3
D42V9, continuous
D42V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P LOSS CNV             1        0         2         0         0         0
  2P LOSS WILD-TYPE      29        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P LOSS CNV                0          0          1        1         0
  2P LOSS WILD-TYPE          9         23         12       16         9
D42V11, multiclass

Clustering(43) Variable = 3p loss
D43V1, survival
                   sevent
clus2                 0   1
  3P LOSS CNV         5   0
  3P LOSS WILD-TYPE 114  11
      3P LOSS CNV 3P LOSS WILD-TYPE 
                5               125 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                0                11 
$`3P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-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-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60         1.81         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-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-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-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 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             0.26              0.16 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            10.19            121.08 
      3P LOSS CNV 3P LOSS WILD-TYPE 
             2.01              6.90 
[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-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS 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-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS 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-3575        TCGA-AG-3581 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr="     "3500000"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          2    6
  3P LOSS WILD-TYPE   72   82
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           2                72
  MALE             6                82
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          5    2
  3P LOSS WILD-TYPE  138   11
                                clus
vv                               3P LOSS CNV 3P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    5               138
  RECTAL MUCINOUS ADENOCARCINOMA           2                11
D43V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          1    7
  3P LOSS WILD-TYPE    5  149
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  NO            1                 5
  YES           7               149
                   vv
clus                 M0  M1 M1A  MX
  3P LOSS CNV         4   3   0   0
  3P LOSS WILD-TYPE 119  19   2  13
D43V6, multiclass
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  M0            4               119
  M1            3                19
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  3P LOSS CNV        3  3   0   0   0  2   0   0  0
  3P LOSS WILD-TYPE 80 32   4   5   1 21   2   7  1
D43V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  3P LOSS CNV         3   0   2   1
  3P LOSS WILD-TYPE 118   2  10   2
D43V8, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  R0           3               118
  R1           0                 2
  R2           2                10
  RX           1                 2
D43V9, continuous
D43V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P LOSS CNV             0        1         2         0         0         0
  3P LOSS WILD-TYPE      30        7        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P LOSS CNV                0          2          0        2         0
  3P LOSS WILD-TYPE          9         21         13       15         9
D43V11, multiclass

Clustering(44) Variable = 3q loss
D44V1, survival
                   sevent
clus2                 0   1
  3Q LOSS CNV         3   0
  3Q LOSS WILD-TYPE 116  11
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3               127 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                0                11 
$`3Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-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-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-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-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 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             0.26              0.16 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            10.19            121.08 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             2.01              6.35 
[1] "0.3 - 10.2 (2.0)"  "0.2 - 121.1 (6.3)"
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS 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-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS 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-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS 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-3575        TCGA-AG-3581 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"3Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          1    3
  3Q LOSS WILD-TYPE   73   85
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           1                73
  MALE             3                85
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          1    3
  3Q LOSS WILD-TYPE  142   10
                                clus
vv                               3Q LOSS CNV 3Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    1               142
  RECTAL MUCINOUS ADENOCARCINOMA           3                10
D44V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          1    3
  3Q LOSS WILD-TYPE    5  153
     clus
vv    3Q LOSS CNV 3Q LOSS WILD-TYPE
  NO            1                 5
  YES           3               153
                   vv
clus                 M0  M1 M1A  MX
  3Q LOSS CNV         2   1   0   0
  3Q LOSS WILD-TYPE 121  21   2  13
D44V6, multiclass
     clus
vv    3Q LOSS CNV 3Q LOSS WILD-TYPE
  M0            2               121
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  3Q LOSS CNV        2  1   0   0   0  1   0   0  0
  3Q LOSS WILD-TYPE 81 34   4   5   1 22   2   7  1
D44V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS CNV         2   0   1   1
  3Q LOSS WILD-TYPE 119   2  11   2
D44V8, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  R0           2               119
  R1           0                 2
  R2           1                11
  RX           1                 2
D44V9, continuous
D44V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q LOSS CNV             0        1         1         0         0         0
  3Q LOSS WILD-TYPE      30        7        37         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q LOSS CNV                0          1          0        1         0
  3Q LOSS WILD-TYPE          9         22         13       16         9
D44V11, multiclass

Clustering(45) Variable = 4p loss
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS CNV       26  1
  4P LOSS WILD-TYPE 93 10
      4P LOSS CNV 4P LOSS WILD-TYPE 
               27               103 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                10 
$`4P LOSS CNV`
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3883 TCGA-AG-3999 
       17.62        14.50         7.59         1.02         1.02         1.02 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02X 
       13.91        25.94        23.01        12.00        70.03        40.96 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
        0.69        10.19         6.02         6.97         6.97        19.99 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
      121.08        32.58         2.40         6.90         6.15         2.76 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 
        0.85         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-3575 
       12.72        10.39         8.45         6.35         7.33        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02         1.02         0.99         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.96         0.95         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-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-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-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-A032 
       51.98        49.94         1.94        38.93        61.94        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        0.49         1.45         0.72         4.60         1.81         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-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       27.91         5.92         3.98         5.00         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.33        57.24        24.13        51.48         0.49         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-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-7004 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
        2.04         3.39         0.39         1.02         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.76         0.46        18.25        47.70        47.08 
TCGA-G5-6641 
       20.91 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             0.69              0.16 
      4P LOSS CNV 4P LOSS WILD-TYPE 
           121.08            119.51 
      4P LOSS CNV 4P LOSS WILD-TYPE 
             6.97              5.92 
[1] "0.7 - 121.1 (7.0)" "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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE" "4P LOSS 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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE" "4P LOSS 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 CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "3"  
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV         16   23
  4P LOSS WILD-TYPE   58   65
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  FEMALE          16                58
  MALE            23                65
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV         36    1
  4P LOSS WILD-TYPE  107   12
                                clus
vv                               4P LOSS CNV 4P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   36               107
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D45V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          3   36
  4P LOSS WILD-TYPE    3  120
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  NO            3                 3
  YES          36               120
                   vv
clus                M0 M1 M1A MX
  4P LOSS CNV       29  5   1  3
  4P LOSS WILD-TYPE 94 17   1 10
D45V6, multiclass
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  M0           29                94
  M1            5                17
  M1A           1                 1
  MX            3                10
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  4P LOSS CNV       17 11   0   1   0  7   0   3  0
  4P LOSS WILD-TYPE 66 24   4   4   1 16   2   4  1
D45V7, multiclass
                   vv
clus                R0 R1 R2 RX
  4P LOSS CNV       32  0  1  0
  4P LOSS WILD-TYPE 89  2 11  3
D45V8, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  R0          32                89
  R1           0                 2
  R2           1                11
  RX           0                 3
D45V9, continuous
D45V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P LOSS CNV             6        1        10         0         0         1
  4P LOSS WILD-TYPE      24        7        28         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P LOSS CNV                2          7          5        3         4
  4P LOSS WILD-TYPE          7         16          8       14         5
D45V11, multiclass

Clustering(46) Variable = 4q loss
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS CNV       33  1
  4Q LOSS WILD-TYPE 86 10
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               34                96 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                1                10 
$`4Q LOSS CNV`
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-3883 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
        1.02         1.02        13.91        25.94        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6620 
       70.03        63.98        40.96         0.69        10.19         6.02 
TCGA-DC-4749 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DE TCGA-DY-A1H8 
       11.01         6.97         6.97        19.99       121.08        32.58 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 
        2.40         8.22         6.90         6.15         2.76         0.85 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        2.17         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-3575 TCGA-AG-3581 TCGA-AG-3583 
        8.45         6.35         7.33        12.00         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.94         6.02        17.03        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        1.02        12.00        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       38.93        61.94        38.01         0.49         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        4.60         1.81         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       13.97        60.00         7.99        10.98         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-6510 TCGA-EI-6511 
        0.49         7.63         0.16         2.17         0.46         3.98 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        0.66         7.10         3.55         3.98         2.73         5.23 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        7.79         2.04         3.39         0.39         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 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             0.66              0.16 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
           121.08            119.51 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            7.905             5.130 
[1] "0.7 - 121.1 (7.9)" "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 CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE" "4Q LOSS 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 CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE" "4Q LOSS 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 CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV"       "4Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
      "4Q LOSS CNV"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "4.6"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV         18   28
  4Q LOSS WILD-TYPE   56   60
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  FEMALE          18                56
  MALE            28                60
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV         41    1
  4Q LOSS WILD-TYPE  102   12
                                clus
vv                               4Q LOSS CNV 4Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   41               102
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D46V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          3   43
  4Q LOSS WILD-TYPE    3  113
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  NO            3                 3
  YES          43               113
                   vv
clus                M0 M1 M1A MX
  4Q LOSS CNV       35  5   1  4
  4Q LOSS WILD-TYPE 88 17   1  9
D46V6, multiclass
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  M0           35                88
  M1            5                17
  M1A           1                 1
  MX            4                 9
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  4Q LOSS CNV       22 12   0   1   0  7   0   4  0
  4Q LOSS WILD-TYPE 61 23   4   4   1 16   2   3  1
D46V7, multiclass
                   vv
clus                R0 R1 R2 RX
  4Q LOSS CNV       36  0  2  0
  4Q LOSS WILD-TYPE 85  2 10  3
D46V8, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  R0          36                85
  R1           0                 2
  R2           2                10
  RX           0                 3
D46V9, continuous
D46V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q LOSS CNV             8        2        12         0         0         1
  4Q LOSS WILD-TYPE      22        6        26         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q LOSS CNV                2          8          6        3         4
  4Q LOSS WILD-TYPE          7         15          7       14         5
D46V11, multiclass

Clustering(47) Variable = 5p loss
D47V1, survival
                   sevent
clus2                 0   1
  5P LOSS CNV         6   0
  5P LOSS WILD-TYPE 113  11
      5P LOSS CNV 5P LOSS WILD-TYPE 
                6               124 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                0                11 
$`5P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       63.98        10.98        51.98        49.94         1.94        38.93 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.94        40.96        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-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-6156 
       10.98        11.01         9.99         5.03         8.98         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-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-6917 TCGA-EI-7002 
        6.15         3.55         3.98         2.73         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 

      5P LOSS CNV 5P LOSS WILD-TYPE 
             1.02              0.16 
      5P LOSS CNV 5P LOSS WILD-TYPE 
           119.51            121.08 
      5P LOSS CNV 5P LOSS WILD-TYPE 
           13.445             6.085 
[1] "1.0 - 119.5 (13.4)" "0.2 - 121.1 (6.1)" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "5P LOSS CNV" "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-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "5P LOSS CNV" "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-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "5P LOSS CNV" "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-3575        TCGA-AG-3581 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"       "5P LOSS CNV" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          8    3
  5P LOSS WILD-TYPE   66   85
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  FEMALE           8                66
  MALE             3                85
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV         11    0
  5P LOSS WILD-TYPE  132   13
                                clus
vv                               5P LOSS CNV 5P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   11               132
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D47V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          1   10
  5P LOSS WILD-TYPE    5  146
     clus
vv    5P LOSS CNV 5P LOSS WILD-TYPE
  NO            1                 5
  YES          10               146
                   vv
clus                 M0  M1 M1A  MX
  5P LOSS CNV         9   2   0   0
  5P LOSS WILD-TYPE 114  20   2  13
D47V6, multiclass
     clus
vv    5P LOSS CNV 5P LOSS WILD-TYPE
  M0            9               114
  M1            2                20
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  5P LOSS CNV        5  0   0   2   0  4   0   0  0
  5P LOSS WILD-TYPE 78 35   4   3   1 19   2   7  1
D47V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  5P LOSS CNV         9   0   1   0
  5P LOSS WILD-TYPE 112   2  11   3
D47V8, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  R0           9               112
  R1           0                 2
  R2           1                11
  RX           0                 3
D47V9, continuous
D47V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P LOSS CNV             1        1         3         0         0         0
  5P LOSS WILD-TYPE      29        7        35         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P LOSS CNV                1          0          3        2         0
  5P LOSS WILD-TYPE          8         23         10       15         9
D47V11, multiclass

Clustering(48) Variable = 5q loss
D48V1, survival
                   sevent
clus2                 0   1
  5Q LOSS CNV        11   3
  5Q LOSS WILD-TYPE 108   8
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               14               116 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                3                 8 
$`5Q LOSS CNV`
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-3575 
       10.39        14.50         8.45         7.59         6.35        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-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-A020 TCGA-AG-A023 
        1.02         1.02        12.00        12.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.94        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-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-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-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        0.26        41.33       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-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        3.39         0.85         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 

      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             1.02              0.16 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
           119.51            121.08 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
           13.905             5.970 
[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 CNV" "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 CNV" 
       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-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "5Q LOSS CNV" "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 CNV" 
       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-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
      "5Q LOSS CNV" "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 CNV" 
       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-3575        TCGA-AG-3581 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"5Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV         13   10
  5Q LOSS WILD-TYPE   61   78
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  FEMALE          13                61
  MALE            10                78
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV         21    1
  5Q LOSS WILD-TYPE  122   12
                                clus
vv                               5Q LOSS CNV 5Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   21               122
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D48V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          4   19
  5Q LOSS WILD-TYPE    2  137
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  NO            4                 2
  YES          19               137
                   vv
clus                 M0  M1 M1A  MX
  5Q LOSS CNV        16   3   1   2
  5Q LOSS WILD-TYPE 107  19   1  11
D48V6, multiclass
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  M0           16               107
  M1            3                19
  M1A           1                 1
  MX            2                11
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  5Q LOSS CNV       11  5   0   1   0  4   0   2  0
  5Q LOSS WILD-TYPE 72 30   4   4   1 19   2   5  1
D48V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS CNV        15   1   1   0
  5Q LOSS WILD-TYPE 106   1  11   3
D48V8, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  R0          15               106
  R1           1                 1
  R2           1                11
  RX           0                 3
D48V9, continuous
D48V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q LOSS CNV             2        3         6         0         0         0
  5Q LOSS WILD-TYPE      28        5        32         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q LOSS CNV                1          3          3        2         3
  5Q LOSS WILD-TYPE          8         20         10       15         6
D48V11, multiclass

Clustering(49) Variable = 6p loss
D49V1, survival
                   sevent
clus2                 0   1
  6P LOSS CNV         5   1
  6P LOSS WILD-TYPE 114  10
      6P LOSS CNV 6P LOSS WILD-TYPE 
                6               124 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                1                10 
$`6P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-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-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-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.00       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-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 

      6P LOSS CNV 6P LOSS WILD-TYPE 
             0.26              0.16 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            24.13            121.08 
      6P LOSS CNV 6P LOSS WILD-TYPE 
           13.730             6.085 
[1] "0.3 - 24.1 (13.7)" "0.2 - 121.1 (6.1)"
       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 CNV" "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-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
      "6P LOSS CNV" "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-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
      "6P LOSS CNV" "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-3575        TCGA-AG-3581 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "5.6"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          4    4
  6P LOSS WILD-TYPE   70   84
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  FEMALE           4                70
  MALE             4                84
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          5    2
  6P LOSS WILD-TYPE  138   11
                                clus
vv                               6P LOSS CNV 6P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    5               138
  RECTAL MUCINOUS ADENOCARCINOMA           2                11
D49V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          0    8
  6P LOSS WILD-TYPE    6  148
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  NO            0                 6
  YES           8               148
                   vv
clus                 M0  M1 M1A  MX
  6P LOSS CNV         7   1   0   0
  6P LOSS WILD-TYPE 116  21   2  13
D49V6, multiclass
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  M0            7               116
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  6P LOSS CNV        6  0   0   0   0  2   0   0  0
  6P LOSS WILD-TYPE 77 35   4   5   1 21   2   7  1
D49V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  6P LOSS CNV         5   0   1   1
  6P LOSS WILD-TYPE 116   2  11   2
D49V8, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  R0           5               116
  R1           0                 2
  R2           1                11
  RX           1                 2
D49V9, continuous
D49V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P LOSS CNV             1        1         3         0         1         0
  6P LOSS WILD-TYPE      29        7        35         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P LOSS CNV                0          0          1        1         0
  6P LOSS WILD-TYPE          9         23         12       16         9
D49V11, multiclass

Clustering(50) Variable = 6q loss
D50V1, survival
                   sevent
clus2                 0   1
  6Q LOSS CNV         8   0
  6Q LOSS WILD-TYPE 111  11
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                8               122 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                0                11 
$`6Q LOSS CNV`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AG-3575 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 
       13.55        19.10        12.00        13.91        17.03         0.49 
TCGA-DT-5265 TCGA-EI-6883 
        0.26         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-3586 TCGA-AG-3587 TCGA-AG-3599 
        1.02         1.02         2.01         1.02         1.02         0.99 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        0.99         7.96         0.95         1.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
        1.02         1.02         1.02         1.02         0.99        20.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.94        23.01        15.91        13.02         1.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        12.00        70.03        63.98        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AH-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-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-DY-A0XA TCGA-DY-A1DC 
       19.99         5.92         3.98         5.00       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-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 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             0.26              0.16 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            19.10            121.08 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
           12.775             6.085 
[1] "0.3 - 19.1 (12.8)" "0.2 - 121.1 (6.1)"
       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 CNV"       "6Q LOSS CNV" "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-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE" "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 CNV"       "6Q LOSS CNV" "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-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE" "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 CNV"       "6Q LOSS CNV" "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-3575        TCGA-AG-3581 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr="     "2.8e+07"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          5    9
  6Q LOSS WILD-TYPE   69   79
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  FEMALE           5                69
  MALE             9                79
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          9    3
  6Q LOSS WILD-TYPE  134   10
                                clus
vv                               6Q LOSS CNV 6Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    9               134
  RECTAL MUCINOUS ADENOCARCINOMA           3                10
D50V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          0   14
  6Q LOSS WILD-TYPE    6  142
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  NO            0                 6
  YES          14               142
                   vv
clus                 M0  M1 M1A  MX
  6Q LOSS CNV        10   3   0   1
  6Q LOSS WILD-TYPE 113  19   2  12
D50V6, multiclass
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           10               113
  M1            3                19
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  6Q LOSS CNV        9  1   0   0   0  4   0   0  0
  6Q LOSS WILD-TYPE 74 34   4   5   1 19   2   7  1
D50V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS CNV        10   0   1   1
  6Q LOSS WILD-TYPE 111   2  11   2
D50V8, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  R0          10               111
  R1           0                 2
  R2           1                11
  RX           1                 2
D50V9, continuous
D50V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q LOSS CNV             2        2         4         0         1         0
  6Q LOSS WILD-TYPE      28        6        34         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q LOSS CNV                0          0          2        2         0
  6Q LOSS WILD-TYPE          9         23         11       15         9
D50V11, multiclass

Clustering(51) Variable = 8p loss
D51V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV       41  2
  8P LOSS WILD-TYPE 78  9
      8P LOSS CNV 8P LOSS WILD-TYPE 
               43                87 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                 9 
$`8P LOSS CNV`
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-3605 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3883 
        7.33         1.02         0.99         0.95         0.99         1.02 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y 
        0.99         1.02         1.02         1.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       17.03        15.91         1.02         1.94        38.93        40.96 
TCGA-BM-6198 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 
       10.19        13.97        60.00        10.98        11.01         7.36 
TCGA-DC-6157 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 
       27.91         5.00         0.26       119.51       121.08         2.40 
TCGA-EI-6511 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6813 TCGA-F5-6864 
        3.98         2.76         2.04         0.85         0.69         0.46 
TCGA-G5-6641 
       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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        6.35        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        0.99         7.96         1.02         0.99         0.92         1.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        0.99         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
        6.02        13.02         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
       63.98        10.98        51.98        49.94        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-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 
        6.02         6.02         6.94         9.37         4.70         7.99 
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-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.92         3.98        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-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        0.46         0.66         6.90         7.10         6.15         3.55 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6702 
        3.98         2.73         5.23         7.79         3.39         2.17 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.66         0.53         1.08         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.25        47.70        47.08 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             0.26              0.16 
      8P LOSS CNV 8P LOSS WILD-TYPE 
           121.08             70.03 
      8P LOSS CNV 8P LOSS WILD-TYPE 
             7.36              6.02 
[1] "0.3 - 121.1 (7.4)" "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 CNV"       "8P LOSS CNV" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       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 CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       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 CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       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 CNV" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" 
[1] "hr=" "2.3"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV         24   32
  8P LOSS WILD-TYPE   50   56
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE          24                50
  MALE            32                56
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV         50    4
  8P LOSS WILD-TYPE   93    9
                                clus
vv                               8P LOSS CNV 8P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   50                93
  RECTAL MUCINOUS ADENOCARCINOMA           4                 9
D51V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          4   52
  8P LOSS WILD-TYPE    2  104
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  NO            4                 2
  YES          52               104
                   vv
clus                M0 M1 M1A MX
  8P LOSS CNV       44  5   0  6
  8P LOSS WILD-TYPE 79 17   2  7
D51V6, multiclass
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  M0           44                79
  M1            5                17
  M1A           0                 2
  MX            6                 7
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  8P LOSS CNV       28 12   1   3   0  9   1   2  0
  8P LOSS WILD-TYPE 55 23   3   2   1 14   1   5  1
D51V7, multiclass
                   vv
clus                R0 R1 R2 RX
  8P LOSS CNV       41  1  5  2
  8P LOSS WILD-TYPE 80  1  7  1
D51V8, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  R0          41                80
  R1           1                 1
  R2           5                 7
  RX           2                 1
D51V9, continuous
D51V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P LOSS CNV            10        2        16         0         0         1
  8P LOSS WILD-TYPE      20        6        22         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P LOSS CNV                3          9          7        6         1
  8P LOSS WILD-TYPE          6         14          6       11         8
D51V11, multiclass

Clustering(52) Variable = 8q loss
D52V1, survival
                   sevent
clus2                 0   1
  8Q LOSS CNV         3   0
  8Q LOSS WILD-TYPE 116  11
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                3               127 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                0                11 
$`8Q LOSS CNV`
TCGA-AG-3605 TCGA-AG-A02X TCGA-DC-6157 
        0.99        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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         1.02         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-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-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-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 

      8Q LOSS CNV 8Q LOSS WILD-TYPE 
             0.99              0.16 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
            40.96            121.08 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
            27.91              6.15 
[1] "1.0 - 41.0 (27.9)" "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-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"       "8Q LOSS CNV" "8Q LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          1    2
  8Q LOSS WILD-TYPE   73   86
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  FEMALE           1                73
  MALE             2                86
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          3    0
  8Q LOSS WILD-TYPE  140   13
                                clus
vv                               8Q LOSS CNV 8Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    3               140
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D52V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          0    3
  8Q LOSS WILD-TYPE    6  153
     clus
vv    8Q LOSS CNV 8Q LOSS WILD-TYPE
  NO            0                 6
  YES           3               153
                   vv
clus                 M0  M1 M1A  MX
  8Q LOSS CNV         2   1   0   0
  8Q LOSS WILD-TYPE 121  21   2  13
D52V6, multiclass
     clus
vv    8Q LOSS CNV 8Q LOSS WILD-TYPE
  M0            2               121
  M1            1                21
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  8Q LOSS CNV        2  1   0   0   0  0   0   0  0
  8Q LOSS WILD-TYPE 81 34   4   5   1 23   2   7  1
D52V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS CNV         2   0   1   0
  8Q LOSS WILD-TYPE 119   2  11   3
D52V8, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  R0           2               119
  R1           0                 2
  R2           1                11
  RX           0                 3
D52V9, continuous
D52V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q LOSS CNV             2        0         0         0         0         0
  8Q LOSS WILD-TYPE      28        8        38         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q LOSS CNV                0          0          0        1         0
  8Q LOSS WILD-TYPE          9         23         13       16         9
D52V11, multiclass

Clustering(53) Variable = 9p loss
D53V1, survival
                   sevent
clus2                 0   1
  9P LOSS CNV         5   3
  9P LOSS WILD-TYPE 114   8
      9P LOSS CNV 9P LOSS WILD-TYPE 
                8               122 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                3                 8 
$`9P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 
        6.35         7.33        12.00         1.02         1.02         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-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-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-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-F5-6465 
        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 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             1.94              0.16 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            51.48            121.08 
      9P LOSS CNV 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-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P LOSS 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-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9P LOSS 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-3575        TCGA-AG-3581 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9P LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "4.7"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          5    7
  9P LOSS WILD-TYPE   69   81
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  FEMALE           5                69
  MALE             7                81
D53V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV         11    1
  9P LOSS WILD-TYPE  132   12
                                clus
vv                               9P LOSS CNV 9P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   11               132
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D53V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          0   12
  9P LOSS WILD-TYPE    6  144
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  NO            0                 6
  YES          12               144
                   vv
clus                 M0  M1 M1A  MX
  9P LOSS CNV         8   4   0   0
  9P LOSS WILD-TYPE 115  18   2  13
D53V6, multiclass
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  M0            8               115
  M1            4                18
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  9P LOSS CNV        6  3   0   0   0  3   0   0  0
  9P LOSS WILD-TYPE 77 32   4   5   1 20   2   7  1
D53V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  9P LOSS CNV         6   1   3   0
  9P LOSS WILD-TYPE 115   1   9   3
D53V8, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  R0           6               115
  R1           1                 1
  R2           3                 9
  RX           0                 3
D53V9, continuous
D53V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P LOSS CNV             3        1         2         0         0         0
  9P LOSS WILD-TYPE      27        7        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P LOSS CNV                1          0          1        3         1
  9P LOSS WILD-TYPE          8         23         12       14         8
D53V11, multiclass

Clustering(54) Variable = 9q loss
D54V1, survival
                   sevent
clus2                 0   1
  9Q LOSS CNV         6   2
  9Q LOSS WILD-TYPE 113   9
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                8               122 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                2                 9 
$`9Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
        7.33        12.00         1.02         1.02         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-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-A02N 
       70.03        63.98        10.98        51.98        49.94        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        9.37         4.70        60.00         7.99        10.98         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
        5.03         8.98         7.36         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-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-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-F5-6465 
        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 

      9Q LOSS CNV 9Q LOSS WILD-TYPE 
             1.94              0.16 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            38.93            121.08 
      9Q LOSS CNV 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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q LOSS 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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"9Q LOSS 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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"9Q LOSS 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-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "7.4"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          5    6
  9Q LOSS WILD-TYPE   69   82
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  FEMALE           5                69
  MALE             6                82
D54V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          9    1
  9Q LOSS WILD-TYPE  134   12
                                clus
vv                               9Q LOSS CNV 9Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    9               134
  RECTAL MUCINOUS ADENOCARCINOMA           1                12
D54V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          0   11
  9Q LOSS WILD-TYPE    6  145
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  NO            0                 6
  YES          11               145
                   vv
clus                 M0  M1 M1A  MX
  9Q LOSS CNV         9   2   0   0
  9Q LOSS WILD-TYPE 114  20   2  13
D54V6, multiclass
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  M0            9               114
  M1            2                20
  M1A           0                 2
  MX            0                13
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  9Q LOSS CNV        7  3   0   0   0  1   0   0  0
  9Q LOSS WILD-TYPE 76 32   4   5   1 22   2   7  1
D54V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS CNV         6   1   3   0
  9Q LOSS WILD-TYPE 115   1   9   3
D54V8, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  R0           6               115
  R1           1                 1
  R2           3                 9
  RX           0                 3
D54V9, continuous
D54V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q LOSS CNV             3        1         3         0         0         0
  9Q LOSS WILD-TYPE      27        7        35         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q LOSS CNV                1          1          0        2         0
  9Q LOSS WILD-TYPE          8         22         13       15         9
D54V11, multiclass

Clustering(55) Variable = 10p loss
D55V1, survival
                    sevent
clus2                  0   1
  10P LOSS CNV        14   0
  10P LOSS WILD-TYPE 105  11
      10P LOSS CNV 10P LOSS WILD-TYPE 
                14                116 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 0                 11 
$`10P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        6.35        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         0.99         1.02         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.94         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.02         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.94         1.94        38.93        61.94        38.01 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-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-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        8.98         6.97         6.97        19.99         5.92         3.98 
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-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         2.40         7.63         0.16         2.17         8.22 
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-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 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              0.49               0.16 
      10P LOSS CNV 10P LOSS WILD-TYPE 
            121.08             119.51 
      10P LOSS CNV 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-3575 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"10P LOSS 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-3575 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"10P LOSS 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-3575 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"10P LOSS WILD-TYPE" 
[1] "hr="     "2.2e+08"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          8    9
  10P LOSS WILD-TYPE   66   79
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            8                 66
  MALE              9                 79
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV         13    4
  10P LOSS WILD-TYPE  130    9
                                clus
vv                               10P LOSS CNV 10P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    13                130
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D55V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          1   16
  10P LOSS WILD-TYPE    5  140
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  NO             1                  5
  YES           16                140
                    vv
clus                  M0  M1 M1A  MX
  10P LOSS CNV        15   1   0   1
  10P LOSS WILD-TYPE 108  21   2  12
D55V6, multiclass
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  M0            15                108
  M1             1                 21
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  10P LOSS CNV        8  5   0   2   0  0   0   2  0
  10P LOSS WILD-TYPE 75 30   4   3   1 23   2   5  1
D55V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  10P LOSS CNV        14   0   0   0
  10P LOSS WILD-TYPE 107   2  12   3
D55V8, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  R0           14                107
  R1            0                  2
  R2            0                 12
  RX            0                  3
D55V9, continuous
D55V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P LOSS CNV             3        0         4         1         0         1
  10P LOSS WILD-TYPE      27        8        34         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P LOSS CNV                1          4          0        1         1
  10P LOSS WILD-TYPE          8         19         13       16         8
D55V11, multiclass

Clustering(56) Variable = 10q loss
D56V1, survival
                    sevent
clus2                  0   1
  10Q LOSS CNV        15   1
  10Q LOSS WILD-TYPE 104  10
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                16                114 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 1                 10 
$`10Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        6.35        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         0.99         1.02         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.94         6.02        25.94        23.01        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        1.02         1.02        12.00        70.03        63.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.94         1.94        38.93        61.94        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-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-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        8.98         6.97         6.97        19.99         5.92         3.98 
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-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.58         2.40         7.63         0.16         2.17         8.22 
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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        3.98         2.73         5.23         7.79         2.04         3.39 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        0.85         2.17         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.08         0.76         0.46        18.25        47.70        20.91 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              0.49               0.16 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
            121.08             119.51 
      10Q LOSS CNV 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-3575 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-G5-6641 
"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-3575 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-G5-6641 
"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-3575 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-G5-6641 
"10Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          8   13
  10Q LOSS WILD-TYPE   66   75
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            8                 66
  MALE             13                 75
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV         17    4
  10Q LOSS WILD-TYPE  126    9
                                clus
vv                               10Q LOSS CNV 10Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    17                126
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D56V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          1   20
  10Q LOSS WILD-TYPE    5  136
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  NO             1                  5
  YES           20                136
                    vv
clus                  M0  M1 M1A  MX
  10Q LOSS CNV        18   1   0   1
  10Q LOSS WILD-TYPE 105  21   2  12
D56V6, multiclass
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  M0            18                105
  M1             1                 21
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  10Q LOSS CNV       11  4   0   2   0  2   0   1  0
  10Q LOSS WILD-TYPE 72 31   4   3   1 21   2   6  1
D56V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS CNV        18   0   0   0
  10Q LOSS WILD-TYPE 103   2  12   3
D56V8, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  R0           18                103
  R1            0                  2
  R2            0                 12
  RX            0                  3
D56V9, continuous
D56V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q LOSS CNV             3        0         7         1         0         1
  10Q LOSS WILD-TYPE      27        8        31         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q LOSS CNV                1          4          1        2         0
  10Q LOSS WILD-TYPE          8         19         12       15         9
D56V11, multiclass

Clustering(57) Variable = 11p loss
D57V1, survival
                    sevent
clus2                  0   1
  11P LOSS CNV        12   1
  11P LOSS WILD-TYPE 107  10
      11P LOSS CNV 11P LOSS WILD-TYPE 
                13                117 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                 10 
$`11P LOSS CNV`
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-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        7.33        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.94         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.02         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.94         1.94        38.93        61.94        38.01 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         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-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.00       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-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-F5-6811 
        2.04         3.39         0.85         2.17         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 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.26               0.16 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             40.96             121.08 
      11P LOSS CNV 11P LOSS WILD-TYPE 
              7.59               6.02 
[1] "0.3 - 41.0 (7.6)"  "0.2 - 121.1 (6.0)"
        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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11P LOSS 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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11P LOSS 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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV         10    9
  11P LOSS WILD-TYPE   64   79
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  FEMALE           10                 64
  MALE              9                 79
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV         14    4
  11P LOSS WILD-TYPE  129    9
                                clus
vv                               11P LOSS CNV 11P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    14                129
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D57V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          1   18
  11P LOSS WILD-TYPE    5  138
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  NO             1                  5
  YES           18                138
                    vv
clus                  M0  M1 M1A  MX
  11P LOSS CNV        17   1   0   1
  11P LOSS WILD-TYPE 106  21   2  12
D57V6, multiclass
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  M0            17                106
  M1             1                 21
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  11P LOSS CNV        8  4   0   2   0  3   0   2  0
  11P LOSS WILD-TYPE 75 31   4   3   1 20   2   5  1
D57V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  11P LOSS CNV        14   0   0   1
  11P LOSS WILD-TYPE 107   2  12   2
D57V8, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  R0           14                107
  R1            0                  2
  R2            0                 12
  RX            1                  2
D57V9, continuous
D57V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P LOSS CNV             4        1         3         0         0         1
  11P LOSS WILD-TYPE      26        7        35         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P LOSS CNV                1          3          5        0         0
  11P LOSS WILD-TYPE          8         20          8       17         9
D57V11, multiclass

Clustering(58) Variable = 11q loss
D58V1, survival
                    sevent
clus2                  0   1
  11Q LOSS CNV        16   1
  11Q LOSS WILD-TYPE 103  10
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                17                113 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                 10 
$`11Q LOSS CNV`
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-3575 TCGA-AG-3582 
       10.39        14.50         8.45         6.35        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.95         1.02         0.99         0.99         1.02         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02         0.99        20.94         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
       38.93        61.94        40.96        38.01         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.70        60.00         7.99        10.98        11.01         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98         6.97        27.91        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-F5-6813 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 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              0.26               0.16 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             24.13             121.08 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              8.22               5.92 
[1] "0.3 - 24.1 (8.2)"  "0.2 - 121.1 (5.9)"
        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 CNV"       "11Q LOSS CNV" 
        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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV         12   11
  11Q LOSS WILD-TYPE   62   77
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  FEMALE           12                 62
  MALE             11                 77
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV         15    5
  11Q LOSS WILD-TYPE  128    8
                                clus
vv                               11Q LOSS CNV 11Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    15                128
  RECTAL MUCINOUS ADENOCARCINOMA            5                  8
D58V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          3   20
  11Q LOSS WILD-TYPE    3  136
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  NO             3                  3
  YES           20                136
                    vv
clus                  M0  M1 M1A  MX
  11Q LOSS CNV        18   1   0   3
  11Q LOSS WILD-TYPE 105  21   2  10
D58V6, multiclass
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  M0            18                105
  M1             1                 21
  M1A            0                  2
  MX             3                 10
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  11Q LOSS CNV       11  6   0   2   0  1   0   3  0
  11Q LOSS WILD-TYPE 72 29   4   3   1 22   2   4  1
D58V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS CNV        15   0   0   1
  11Q LOSS WILD-TYPE 106   2  12   2
D58V8, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  R0           15                106
  R1            0                  2
  R2            0                 12
  RX            1                  2
D58V9, continuous
D58V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q LOSS CNV             5        1         5         0         0         1
  11Q LOSS WILD-TYPE      25        7        33         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q LOSS CNV                2          4          3        1         0
  11Q LOSS WILD-TYPE          7         19         10       16         9
D58V11, multiclass

Clustering(59) Variable = 12p loss
D59V1, survival
                    sevent
clus2                  0   1
  12P LOSS CNV         3   3
  12P LOSS WILD-TYPE 116   8
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 6                124 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 3                  8 
$`12P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.94        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       17.03        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-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-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.00         0.26       119.51        41.33        57.24       121.08 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       32.58         0.49         2.40         7.63         0.16         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-F5-6811 
        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 

      12P LOSS CNV 12P LOSS WILD-TYPE 
              2.17               0.16 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             70.03             121.08 
      12P LOSS CNV 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 CNV" 
        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-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12P LOSS CNV"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P LOSS 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 CNV" 
        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-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12P LOSS CNV"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12P LOSS 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 CNV" 
        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-3575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12P LOSS CNV"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12P LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          9    3
  12P LOSS WILD-TYPE   65   85
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  FEMALE            9                 65
  MALE              3                 85
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV         12    0
  12P LOSS WILD-TYPE  131   13
                                clus
vv                               12P LOSS CNV 12P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    12                131
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D59V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          0   12
  12P LOSS WILD-TYPE    6  144
     clus
vv    12P LOSS CNV 12P LOSS WILD-TYPE
  NO             0                  6
  YES           12                144
                    vv
clus                  M0  M1 M1A  MX
  12P LOSS CNV         9   3   0   0
  12P LOSS WILD-TYPE 114  19   2  13
D59V6, multiclass
     clus
vv    12P LOSS CNV 12P LOSS WILD-TYPE
  M0             9                114
  M1             3                 19
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  12P LOSS CNV        4  2   2   1   0  3   0   0  0
  12P LOSS WILD-TYPE 79 33   2   4   1 20   2   7  1
D59V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  12P LOSS CNV         9   0   1   0
  12P LOSS WILD-TYPE 112   2  11   3
D59V8, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  R0            9                112
  R1            0                  2
  R2            1                 11
  RX            0                  3
D59V9, continuous
D59V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P LOSS CNV             0        1         3         0         0         0
  12P LOSS WILD-TYPE      30        7        35         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P LOSS CNV                1          2          2        1         1
  12P LOSS WILD-TYPE          8         21         11       16         8
D59V11, multiclass

Clustering(60) Variable = 12q loss
D60V1, survival
                    sevent
clus2                  0   1
  12Q LOSS CNV         3   2
  12Q LOSS WILD-TYPE 116   9
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 5                125 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 2                  9 
$`12Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        17.03        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.93        61.94        40.96        38.01         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-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.00         0.26       119.51        41.33        57.24       121.08 
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 

      12Q LOSS CNV 12Q LOSS WILD-TYPE 
              0.49               0.16 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
             51.48             121.08 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
             15.91               6.02 
[1] "0.5 - 51.5 (15.9)" "0.2 - 121.1 (6.0)"
        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-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12Q LOSS CNV"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q LOSS 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-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12Q LOSS CNV"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"12Q LOSS 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-3575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "12Q LOSS CNV"       "12Q LOSS CNV" "12Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "3.5"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          4    4
  12Q LOSS WILD-TYPE   70   84
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  FEMALE            4                 70
  MALE              4                 84
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          8    0
  12Q LOSS WILD-TYPE  135   13
                                clus
vv                               12Q LOSS CNV 12Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     8                135
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D60V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          0    8
  12Q LOSS WILD-TYPE    6  148
     clus
vv    12Q LOSS CNV 12Q LOSS WILD-TYPE
  NO             0                  6
  YES            8                148
                    vv
clus                  M0  M1 M1A  MX
  12Q LOSS CNV         5   3   0   0
  12Q LOSS WILD-TYPE 118  19   2  13
D60V6, multiclass
     clus
vv    12Q LOSS CNV 12Q LOSS WILD-TYPE
  M0             5                118
  M1             3                 19
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  12Q LOSS CNV        2  3   0   1   0  2   0   0  0
  12Q LOSS WILD-TYPE 81 32   4   4   1 21   2   7  1
D60V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS CNV         4   0   1   0
  12Q LOSS WILD-TYPE 117   2  11   3
D60V8, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            1                 11
  RX            0                  3
D60V9, continuous
D60V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q LOSS CNV             1        0         1         0         0         0
  12Q LOSS WILD-TYPE      29        8        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q LOSS CNV                1          1          1        1         1
  12Q LOSS WILD-TYPE          8         22         12       16         8
D60V11, multiclass

Clustering(61) Variable = 13q loss
D61V1, survival
                    sevent
clus2                  0   1
  13Q LOSS CNV         2   0
  13Q LOSS WILD-TYPE 117  11
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                128 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 0                 11 
$`13Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98         7.36        27.91         6.97        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.92         3.98         5.00         0.26        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 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              6.97               0.16 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
            119.51             121.08 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
            63.240              6.085 
[1] "7.0 - 119.5 (63.2)" "0.2 - 121.1 (6.1)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"13Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                128 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A1DC         TCGA-DY-A1DD 
"13Q LOSS WILD-TYPE" "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" 
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          2    3
  13Q LOSS WILD-TYPE   72   85
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            2                 72
  MALE              3                 85
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          4    1
  13Q LOSS WILD-TYPE  139   12
                                clus
vv                               13Q LOSS CNV 13Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     4                139
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D61V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          0    5
  13Q LOSS WILD-TYPE    6  151
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  NO             0                  6
  YES            5                151
                    vv
clus                  M0  M1 M1A  MX
  13Q LOSS CNV         4   0   1   0
  13Q LOSS WILD-TYPE 119  22   1  13
D61V6, multiclass
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0             4                119
  M1             0                 22
  M1A            1                  1
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  13Q LOSS CNV        3  0   0   0   0  1   0   1  0
  13Q LOSS WILD-TYPE 80 35   4   5   1 22   2   6  1
D61V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS CNV         4   0   0   0
  13Q LOSS WILD-TYPE 117   2  12   3
D61V8, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            0                 12
  RX            0                  3
D61V9, continuous
D61V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q LOSS CNV             0        0         3         0         0         0
  13Q LOSS WILD-TYPE      30        8        35         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q LOSS CNV                0          0          1        0         1
  13Q LOSS WILD-TYPE          9         23         12       17         8
D61V11, multiclass

Clustering(62) Variable = 14q loss
D62V1, survival
                    sevent
clus2                 0  1
  14Q LOSS CNV       37  3
  14Q LOSS WILD-TYPE 82  8
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                40                 90 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 3                  8 
$`14Q LOSS CNV`
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-3883 TCGA-AG-3893 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00C 
        0.99         1.02         0.99         1.02         1.02         6.02 
TCGA-AG-A00H TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 
       25.94         1.94        38.93        38.01         0.49        10.19 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        6.02         9.37        13.97         7.99        11.01         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG 
        7.36        27.91         6.97         5.00       121.08        51.48 
TCGA-EI-6506 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 
        7.63         6.90         7.10         6.15         2.73         2.76 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        0.85         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-3575 TCGA-AG-3581 
        8.45         7.59         6.35         7.33        12.00         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 
        2.01         1.02         1.02         0.99         0.99         7.96 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02         0.99         0.92         1.02         0.99         1.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y 
        1.02         1.02         0.99        20.94        13.91        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-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.94        40.96         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
        1.81         6.02         6.94         4.70        60.00        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        9.99         8.98         6.97        19.99         5.92         3.98 
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-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
        3.98         0.66         3.55         3.98         5.23         7.79 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        2.04         3.39         2.17         0.69         0.53         1.08 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.25        47.70        47.08        20.91 

      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              0.39               0.16 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
            121.08             119.51 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             6.525              6.185 
[1] "0.4 - 121.1 (6.5)" "0.2 - 119.5 (6.2)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"14Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"14Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"14Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV         22   29
  14Q LOSS WILD-TYPE   52   59
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  FEMALE           22                 52
  MALE             29                 59
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV         49    0
  14Q LOSS WILD-TYPE   94   13
                                clus
vv                               14Q LOSS CNV 14Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    49                 94
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D62V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          2   49
  14Q LOSS WILD-TYPE    4  107
     clus
vv    14Q LOSS CNV 14Q LOSS WILD-TYPE
  NO             2                  4
  YES           49                107
                    vv
clus                 M0 M1 M1A MX
  14Q LOSS CNV       40  8   0  2
  14Q LOSS WILD-TYPE 83 14   2 11
D62V6, multiclass
     clus
vv    14Q LOSS CNV 14Q LOSS WILD-TYPE
  M0            40                 83
  M1             8                 14
  M1A            0                  2
  MX             2                 11
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  14Q LOSS CNV       26 15   1   2   0  7   0   0  0
  14Q LOSS WILD-TYPE 57 20   3   3   1 16   2   7  1
D62V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS CNV       37  1  3  1
  14Q LOSS WILD-TYPE 84  1  9  2
D62V8, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  R0           37                 84
  R1            1                  1
  R2            3                  9
  RX            1                  2
D62V9, continuous
D62V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q LOSS CNV             7        1        18         0         0         1
  14Q LOSS WILD-TYPE      23        7        20         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q LOSS CNV                4          8          3        5         2
  14Q LOSS WILD-TYPE          5         15         10       12         7
D62V11, multiclass

Clustering(63) Variable = 15q loss
D63V1, survival
                    sevent
clus2                 0  1
  15Q LOSS CNV       37  5
  15Q LOSS WILD-TYPE 82  6
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                42                 88 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 5                  6 
$`15Q LOSS CNV`
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-3575 TCGA-AG-3581 
       10.39         8.45         7.59         6.35        12.00         1.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
        1.02         1.02         1.02         0.99        20.94         6.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.91        13.02         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       63.98        10.98        51.98        49.94        61.94         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-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-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-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
        3.98         5.00         0.26       119.51       121.08        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.58         7.63         0.16         2.17         8.22         0.46 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        0.66         6.90         3.55         7.79         2.04         3.39 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        2.17         0.39         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 

      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              0.49               0.16 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
             57.24             121.08 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
             5.690              6.625 
[1] "0.5 - 57.2 (5.7)"  "0.2 - 121.1 (6.6)"
        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 CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"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 CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"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 CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV"       "15Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "15Q LOSS CNV"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"15Q LOSS WILD-TYPE" 
[1] "hr=" "3"  
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV         24   34
  15Q LOSS WILD-TYPE   50   54
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  FEMALE           24                 50
  MALE             34                 54
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV         51    4
  15Q LOSS WILD-TYPE   92    9
                                clus
vv                               15Q LOSS CNV 15Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    51                 92
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D63V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          3   55
  15Q LOSS WILD-TYPE    3  101
     clus
vv    15Q LOSS CNV 15Q LOSS WILD-TYPE
  NO             3                  3
  YES           55                101
                    vv
clus                 M0 M1 M1A MX
  15Q LOSS CNV       44  8   0  5
  15Q LOSS WILD-TYPE 79 14   2  8
D63V6, multiclass
     clus
vv    15Q LOSS CNV 15Q LOSS WILD-TYPE
  M0            44                 79
  M1             8                 14
  M1A            0                  2
  MX             5                  8
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  15Q LOSS CNV       28 15   0   2   0 10   0   3  0
  15Q LOSS WILD-TYPE 55 20   4   3   1 13   2   4  1
D63V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS CNV       42  1  4  1
  15Q LOSS WILD-TYPE 79  1  8  2
D63V8, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  R0           42                 79
  R1            1                  1
  R2            4                  8
  RX            1                  2
D63V9, continuous
D63V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q LOSS CNV             6        1        19         1         1         2
  15Q LOSS WILD-TYPE      24        7        19         1         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q LOSS CNV                3          9          6        8         1
  15Q LOSS WILD-TYPE          6         14          7        9         8
D63V11, multiclass

Clustering(64) Variable = 16p loss
D64V1, survival
                    sevent
clus2                  0   1
  16P LOSS CNV         2   0
  16P LOSS WILD-TYPE 117  11
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                128 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 0                 11 
$`16P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01         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 

      16P LOSS CNV 16P LOSS WILD-TYPE 
              1.02               0.16 
      16P LOSS CNV 16P LOSS WILD-TYPE 
              3.98             121.08 
      16P LOSS CNV 16P LOSS WILD-TYPE 
             2.500              6.625 
[1] "1.0 - 4.0 (2.5)"   "0.2 - 121.1 (6.6)"
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "16P LOSS CNV"          
clus
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 2                128 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6683 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-EI-7004 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F5-6810         TCGA-F5-6812         TCGA-F5-6813 
"16P LOSS WILD-TYPE" "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" 
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          4    2
  16P LOSS WILD-TYPE   70   86
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  FEMALE            4                 70
  MALE              2                 86
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          4    1
  16P LOSS WILD-TYPE  139   12
                                clus
vv                               16P LOSS CNV 16P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     4                139
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D64V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          0    6
  16P LOSS WILD-TYPE    6  150
     clus
vv    16P LOSS CNV 16P LOSS WILD-TYPE
  NO             0                  6
  YES            6                150
                    vv
clus                  M0  M1 M1A  MX
  16P LOSS CNV         5   1   0   0
  16P LOSS WILD-TYPE 118  21   2  13
D64V6, multiclass
     clus
vv    16P LOSS CNV 16P LOSS WILD-TYPE
  M0             5                118
  M1             1                 21
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  16P LOSS CNV        5  0   0   0   0  1   0   0  0
  16P LOSS WILD-TYPE 78 35   4   5   1 22   2   7  1
D64V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  16P LOSS CNV         4   0   0   0
  16P LOSS WILD-TYPE 117   2  12   3
D64V8, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            0                 12
  RX            0                  3
D64V9, continuous
D64V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P LOSS CNV             0        0         5         0         0         0
  16P LOSS WILD-TYPE      30        8        33         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P LOSS CNV                0          0          0        1         0
  16P LOSS WILD-TYPE          9         23         13       16         9
D64V11, multiclass

Clustering(65) Variable = 16q loss
D65V1, survival
                    sevent
clus2                  0   1
  16Q LOSS CNV         4   0
  16Q LOSS WILD-TYPE 115  11
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 4                126 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 0                 11 
$`16Q LOSS CNV`
TCGA-AF-6672 TCGA-AG-3883 TCGA-DC-6682 TCGA-F5-6811 
        7.33         1.02         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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        6.35        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         0.99         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-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-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-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        2.17         0.39         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 

      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              1.02               0.16 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              7.33             121.08 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             2.500              6.625 
[1] "1.0 - 7.3 (2.5)"   "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-3575 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS 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-3883         TCGA-AG-3887         TCGA-AG-3892 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS 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-3883         TCGA-AG-3887         TCGA-AG-3892 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"16Q LOSS WILD-TYPE" "16Q LOSS 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-3883         TCGA-AG-3887         TCGA-AG-3892 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"16Q LOSS WILD-TYPE" 
[1] "hr="     "3400000"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          5    5
  16Q LOSS WILD-TYPE   69   83
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  FEMALE            5                 69
  MALE              5                 83
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          8    1
  16Q LOSS WILD-TYPE  135   12
                                clus
vv                               16Q LOSS CNV 16Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     8                135
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D65V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          1    9
  16Q LOSS WILD-TYPE    5  147
     clus
vv    16Q LOSS CNV 16Q LOSS WILD-TYPE
  NO             1                  5
  YES            9                147
                    vv
clus                  M0  M1 M1A  MX
  16Q LOSS CNV         8   1   0   1
  16Q LOSS WILD-TYPE 115  21   2  12
D65V6, multiclass
     clus
vv    16Q LOSS CNV 16Q LOSS WILD-TYPE
  M0             8                115
  M1             1                 21
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  16Q LOSS CNV        7  0   0   0   0  2   0   1  0
  16Q LOSS WILD-TYPE 76 35   4   5   1 21   2   6  1
D65V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS CNV         7   0   0   0
  16Q LOSS WILD-TYPE 114   2  12   3
D65V8, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  R0            7                114
  R1            0                  2
  R2            0                 12
  RX            0                  3
D65V9, continuous
D65V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q LOSS CNV             2        0         5         0         0         0
  16Q LOSS WILD-TYPE      28        8        33         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q LOSS CNV                0          0          1        2         0
  16Q LOSS WILD-TYPE          9         23         12       15         9
D65V11, multiclass

Clustering(66) Variable = 17p loss
D66V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV       64  6
  17P LOSS WILD-TYPE 55  5
      17P LOSS CNV 17P LOSS WILD-TYPE 
                70                 60 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 6                  5 
$`17P LOSS CNV`
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-3605 
       14.50         7.59         6.35         1.02         1.02         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 
        7.96         0.95         1.02         0.99         1.02         0.99 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       17.03        15.91         1.02        12.00        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 
       63.98        51.98         1.94        40.96         0.49         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 
        4.60        10.19         6.02         6.94        13.97         7.99 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A0XA 
       11.01         7.36         6.97        19.99         0.26       119.51 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.33        57.24       121.08        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
        2.40         2.17         8.22         6.90         7.10         3.98 
TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
        2.73         2.76         2.04         3.39         0.85         0.39 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.76         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-3575 
       19.53        11.77        10.39         8.45         7.33        12.00 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3878 TCGA-AG-3887 
        2.01         1.02         1.02         0.99         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4022 
        1.02         0.99         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       20.94        13.02         1.02        10.98        49.94        38.93 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6903 TCGA-CI-6619 
       61.94        38.01         1.45         0.69         1.81         6.02 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37         4.70        60.00        10.98         9.99         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        8.98         6.97        27.91         5.92         3.98         5.00 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       32.58         7.63         0.16         0.46         3.98         0.66 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6702 TCGA-F5-6811 
        6.15         3.55         5.23         7.79         2.17         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.66         0.53         1.08        18.25        47.08        20.91 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              0.26               0.16 
      17P LOSS CNV 17P LOSS WILD-TYPE 
            121.08              61.94 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             7.035              5.130 
[1] "0.3 - 121.1 (7.0)" "0.2 - 61.9 (5.1)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         43   46
  17P LOSS WILD-TYPE   31   42
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  FEMALE           43                 31
  MALE             46                 42
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         79    6
  17P LOSS WILD-TYPE   64    7
                                clus
vv                               17P LOSS CNV 17P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    79                 64
  RECTAL MUCINOUS ADENOCARCINOMA            6                  7
D66V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          4   85
  17P LOSS WILD-TYPE    2   71
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  NO             4                  2
  YES           85                 71
                    vv
clus                 M0 M1 M1A MX
  17P LOSS CNV       67 14   0  7
  17P LOSS WILD-TYPE 56  8   2  6
D66V6, multiclass
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  M0            67                 56
  M1            14                  8
  M1A            0                  2
  MX             7                  6
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  17P LOSS CNV       48 20   1   2   0 13   1   3  1
  17P LOSS WILD-TYPE 35 15   3   3   1 10   1   4  0
D66V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  17P LOSS CNV       62  2  8  2
  17P LOSS WILD-TYPE 59  0  4  1
D66V8, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  R0           62                 59
  R1            2                  0
  R2            8                  4
  RX            2                  1
D66V9, continuous
D66V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P LOSS CNV            14        4        26         2         1         2
  17P LOSS WILD-TYPE      16        4        12         0         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P LOSS CNV                4         12          7       11         4
  17P LOSS WILD-TYPE          5         11          6        6         5
D66V11, multiclass

Clustering(67) Variable = 17q loss
D67V1, survival
                    sevent
clus2                  0   1
  17Q LOSS CNV        11   1
  17Q LOSS WILD-TYPE 108  10
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                12                118 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                 10 
$`17Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        7.33        12.00         1.02         2.01         1.02         1.02 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
        0.99         0.99         7.96         0.95         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        1.02         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.94         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.02         1.02         1.02        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.94         1.94        38.93        61.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.01         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-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-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-6157 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98         6.97        27.91        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-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      121.08        51.48        32.58         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 

      17Q LOSS CNV 17Q LOSS WILD-TYPE 
              0.49               0.16 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             40.96             121.08 
      17Q LOSS CNV 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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"       "17Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "17Q LOSS CNV"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"17Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          6    9
  17Q LOSS WILD-TYPE   68   79
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  FEMALE            6                 68
  MALE              9                 79
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV         14    1
  17Q LOSS WILD-TYPE  129   12
                                clus
vv                               17Q LOSS CNV 17Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    14                129
  RECTAL MUCINOUS ADENOCARCINOMA            1                 12
D67V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          2   13
  17Q LOSS WILD-TYPE    4  143
     clus
vv    17Q LOSS CNV 17Q LOSS WILD-TYPE
  NO             2                  4
  YES           13                143
                    vv
clus                  M0  M1 M1A  MX
  17Q LOSS CNV        11   2   0   1
  17Q LOSS WILD-TYPE 112  20   2  12
D67V6, multiclass
     clus
vv    17Q LOSS CNV 17Q LOSS WILD-TYPE
  M0            11                112
  M1             2                 20
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  17Q LOSS CNV        8  3   0   2   0  2   0   0  0
  17Q LOSS WILD-TYPE 75 32   4   3   1 21   2   7  1
D67V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS CNV        11   0   2   0
  17Q LOSS WILD-TYPE 110   2  10   3
D67V8, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  R0           11                110
  R1            0                  2
  R2            2                 10
  RX            0                  3
D67V9, continuous
D67V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q LOSS CNV             3        0         3         1         1         0
  17Q LOSS WILD-TYPE      27        8        35         1         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q LOSS CNV                1          3          1        2         0
  17Q LOSS WILD-TYPE          8         20         12       15         9
D67V11, multiclass

Clustering(68) Variable = 18p loss
D68V1, survival
                    sevent
clus2                 0  1
  18P LOSS CNV       86  7
  18P LOSS WILD-TYPE 33  4
      18P LOSS CNV 18P LOSS WILD-TYPE 
                93                 37 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 7                  4 
$`18P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 
       14.50         7.59         6.35        12.00         1.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3742 TCGA-AG-3883 
        2.01         1.02         0.99         7.96         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.92         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         0.99        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       17.03        15.91         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       70.03        10.98        51.98         1.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6620 
        0.49         0.69         0.72         4.60        10.19         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.94         9.37        13.97        60.00         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01         5.03         8.98         7.36         6.97        27.91 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        6.97        19.99         5.92         5.00       119.51        41.33 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       121.08        24.13        51.48         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
        7.63         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-F5-6465 
        6.15         3.98         2.73         5.23         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-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        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-3586 
       10.62        19.10        12.72         8.45         7.33         1.02 
TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 
        0.99         0.95         1.02         0.99         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       20.94        13.02        63.98        49.94        38.93        61.94 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6682 
        1.45         1.81         6.02         4.70         9.99         3.98 
TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6882 
        0.26        32.58         0.16         2.17         0.46         3.55 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 
        7.79         2.04         0.53         1.08        18.25        47.08 
TCGA-G5-6641 
       20.91 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              0.39               0.16 
      18P LOSS CNV 18P LOSS WILD-TYPE 
            121.08              63.98 
      18P LOSS CNV 18P LOSS WILD-TYPE 
               6.9                4.7 
[1] "0.4 - 121.1 (6.9)" "0.2 - 64.0 (4.7)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"18P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"18P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18P LOSS CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18P LOSS CNV"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18P LOSS WILD-TYPE"       "18P LOSS CNV"       "18P LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"18P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV         53   61
  18P LOSS WILD-TYPE   21   27
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  FEMALE           53                 21
  MALE             61                 27
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV        107    5
  18P LOSS WILD-TYPE   36    8
                                clus
vv                               18P LOSS CNV 18P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   107                 36
  RECTAL MUCINOUS ADENOCARCINOMA            5                  8
D68V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          4  110
  18P LOSS WILD-TYPE    2   46
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  NO             4                  2
  YES          110                 46
                    vv
clus                 M0 M1 M1A MX
  18P LOSS CNV       86 18   2  7
  18P LOSS WILD-TYPE 37  4   0  6
D68V6, multiclass
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  M0            86                 37
  M1            18                  4
  M1A            2                  0
  MX             7                  6
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  18P LOSS CNV       55 27   3   4   0 18   1   5  1
  18P LOSS WILD-TYPE 28  8   1   1   1  5   1   2  0
D68V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  18P LOSS CNV       85  2 10  2
  18P LOSS WILD-TYPE 36  0  2  1
D68V8, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  R0           85                 36
  R1            2                  0
  R2           10                  2
  RX            2                  1
D68V9, continuous
D68V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P LOSS CNV            18        5        28         2         1         2
  18P LOSS WILD-TYPE      12        3        10         0         1         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P LOSS CNV                5         20         10       12         7
  18P LOSS WILD-TYPE          4          3          3        5         2
D68V11, multiclass

Clustering(69) Variable = 18q loss
D69V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV       92  8
  18Q LOSS WILD-TYPE 27  3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
               100                 30 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 8                  3 
$`18Q LOSS CNV`
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-3575 TCGA-AG-3581 
       10.39        14.50         7.59         6.35        12.00         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         7.96         0.95 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
        0.99         1.02         0.92         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-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-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        40.96        38.01         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        4.60        10.19         6.02         6.94         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.00         7.99        10.98        11.01         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-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-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
        3.98         0.66         6.90         7.10         6.15         3.98 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
        2.73         5.23         2.76         2.04         3.39         0.85 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
        2.17         0.39         1.02         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        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-3586 TCGA-AG-3599 
       10.62        12.72         8.45         7.33         1.02         0.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 
        1.02         0.99         1.02         0.99        20.94        13.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6619 
       49.94        38.93        61.94         1.45         1.81         6.02 
TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
        4.70         9.99         3.98         0.26        32.58         0.16 
TCGA-EI-6510 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
        0.46         3.55         7.79         0.53         1.08        18.25 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.39               0.16 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
            121.08              61.94 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              6.92               4.34 
[1] "0.4 - 121.1 (6.9)" "0.2 - 61.9 (4.3)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6641 
      "18Q LOSS CNV" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6641 
      "18Q LOSS CNV" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-G5-6641 
      "18Q LOSS CNV" 
[1] "hr=" "1.8"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV         60   66
  18Q LOSS WILD-TYPE   14   22
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE           60                 14
  MALE             66                 22
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV        113    9
  18Q LOSS WILD-TYPE   30    4
                                clus
vv                               18Q LOSS CNV 18Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                   113                 30
  RECTAL MUCINOUS ADENOCARCINOMA            9                  4
D69V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          4  122
  18Q LOSS WILD-TYPE    2   34
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  NO             4                  2
  YES          122                 34
                    vv
clus                 M0 M1 M1A MX
  18Q LOSS CNV       94 19   2  9
  18Q LOSS WILD-TYPE 29  3   0  4
D69V6, multiclass
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  M0            94                 29
  M1            19                  3
  M1A            2                  0
  MX             9                  4
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  18Q LOSS CNV       61 29   4   4   0 19   1   6  1
  18Q LOSS WILD-TYPE 22  6   0   1   1  4   1   1  0
D69V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS CNV       94  2 10  2
  18Q LOSS WILD-TYPE 27  0  2  1
D69V8, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  R0           94                 27
  R1            2                  0
  R2           10                  2
  RX            2                  1
D69V9, continuous
D69V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q LOSS CNV            19        6        32         2         1         3
  18Q LOSS WILD-TYPE      11        2         6         0         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q LOSS CNV                6         21         10       13         8
  18Q LOSS WILD-TYPE          3          2          3        4         1
D69V11, multiclass

Clustering(70) Variable = 19p loss
D70V1, survival
                    sevent
clus2                  0   1
  19P LOSS CNV         3   2
  19P LOSS WILD-TYPE 116   9
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                125 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                  9 
$`19P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        17.03        15.91        13.02         1.02         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        12.00        70.03        63.98        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.94         1.94        38.93        61.94        40.96        38.01 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.02         6.02         6.94         9.37         4.70 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.00         7.99        10.98        11.01         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98         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-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       121.08        32.58         2.40         7.63         0.16 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
        2.17         8.22         0.46         3.98         0.66         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 

      19P LOSS CNV 19P LOSS WILD-TYPE 
              0.49               0.16 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             51.48             121.08 
      19P LOSS CNV 19P LOSS WILD-TYPE 
              7.36               6.02 
[1] "0.5 - 51.5 (7.4)"  "0.2 - 121.1 (6.0)"
        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-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19P LOSS CNV"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P LOSS 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-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19P LOSS CNV"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19P LOSS 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-3575 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19P LOSS CNV"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19P LOSS WILD-TYPE" 
[1] "hr=" "3.7"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          4    3
  19P LOSS WILD-TYPE   70   85
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  FEMALE            4                 70
  MALE              3                 85
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          6    0
  19P LOSS WILD-TYPE  137   13
                                clus
vv                               19P LOSS CNV 19P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     6                137
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D70V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          0    7
  19P LOSS WILD-TYPE    6  149
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  NO             0                  6
  YES            7                149
                    vv
clus                  M0  M1 M1A  MX
  19P LOSS CNV         6   1   0   0
  19P LOSS WILD-TYPE 117  21   2  13
D70V6, multiclass
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  M0             6                117
  M1             1                 21
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  19P LOSS CNV        3  2   0   1   0  1   0   0  0
  19P LOSS WILD-TYPE 80 33   4   4   1 22   2   7  1
D70V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  19P LOSS CNV         4   0   0   0
  19P LOSS WILD-TYPE 117   2  12   3
D70V8, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  R0            4                117
  R1            0                  2
  R2            0                 12
  RX            0                  3
D70V9, continuous
D70V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P LOSS CNV             0        0         2         1         0         0
  19P LOSS WILD-TYPE      30        8        36         1         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P LOSS CNV                1          1          1        0         1
  19P LOSS WILD-TYPE          8         22         12       17         8
D70V11, multiclass

Clustering(71) Variable = 19q loss
D71V1, survival
                    sevent
clus2                  0   1
  19Q LOSS CNV         4   1
  19Q LOSS WILD-TYPE 115  10
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 5                125 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 1                 10 
$`19Q LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
        6.35         7.33        12.00         1.02         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.99         1.02         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        15.91        13.02         1.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        63.98        10.98        51.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.93        61.94        40.96        38.01         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-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-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       121.08        51.48        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-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 

      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              0.49               0.16 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             24.13             121.08 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              6.90               6.15 
[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-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q LOSS 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-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"19Q LOSS 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-3575 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"19Q LOSS WILD-TYPE" 
[1] "hr=" "7.3"
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          3    4
  19Q LOSS WILD-TYPE   71   84
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  FEMALE            3                 71
  MALE              4                 84
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          6    0
  19Q LOSS WILD-TYPE  137   13
                                clus
vv                               19Q LOSS CNV 19Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                     6                137
  RECTAL MUCINOUS ADENOCARCINOMA            0                 13
D71V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          0    7
  19Q LOSS WILD-TYPE    6  149
     clus
vv    19Q LOSS CNV 19Q LOSS WILD-TYPE
  NO             0                  6
  YES            7                149
                    vv
clus                  M0  M1 M1A  MX
  19Q LOSS CNV         7   0   0   0
  19Q LOSS WILD-TYPE 116  22   2  13
D71V6, multiclass
     clus
vv    19Q LOSS CNV 19Q LOSS WILD-TYPE
  M0             7                116
  M1             0                 22
  M1A            0                  2
  MX             0                 13
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  19Q LOSS CNV        5  1   0   0   0  1   0   0  0
  19Q LOSS WILD-TYPE 78 34   4   5   1 22   2   7  1
D71V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS CNV         5   0   0   0
  19Q LOSS WILD-TYPE 116   2  12   3
D71V8, multiclass
    clus
vv   19Q LOSS CNV 19Q LOSS WILD-TYPE
  R0            5                116
  R1            0                  2
  R2            0                 12
  RX            0                  3
D71V9, continuous
D71V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q LOSS CNV             0        0         3         1         1         0
  19Q LOSS WILD-TYPE      30        8        35         1         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q LOSS CNV                0          1          1        0         0
  19Q LOSS WILD-TYPE          9         22         12       17         9
D71V11, multiclass

Clustering(72) Variable = 20p loss
D72V1, survival
                    sevent
clus2                  0   1
  20P LOSS CNV        11   2
  20P LOSS WILD-TYPE 108   9
      20P LOSS CNV 20P LOSS WILD-TYPE 
                13                117 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                  9 
$`20P LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.94         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       13.02         1.02        10.98        51.98        49.94        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       40.96        38.01         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.02         6.02         6.94 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.70        13.97        60.00         7.99        10.98 
TCGA-DC-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-DT-5265 
       27.91         6.97        19.99         5.92         3.98         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-6514 
        8.22         0.46         3.98         0.66         6.90         7.10 
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 

      20P LOSS CNV 20P LOSS WILD-TYPE 
              0.99               0.16 
      20P LOSS CNV 20P LOSS WILD-TYPE 
             70.03             121.08 
      20P LOSS CNV 20P LOSS WILD-TYPE 
             12.00               6.02 
[1] "1.0 - 70.0 (12.0)" "0.2 - 121.1 (6.0)"
        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 CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20P LOSS CNV"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"20P LOSS 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 CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20P LOSS CNV"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"20P LOSS 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 CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"20P LOSS WILD-TYPE"       "20P LOSS CNV" "20P LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "20P LOSS CNV"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"20P LOSS WILD-TYPE"       "20P LOSS CNV"       "20P LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G5-6641 
"20P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          9    9
  20P LOSS WILD-TYPE   65   79
        clus
vv       20P LOSS CNV 20P LOSS WILD-TYPE
  FEMALE            9                 65
  MALE              9                 79
D72V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV         15    2
  20P LOSS WILD-TYPE  128   11
                                clus
vv                               20P LOSS CNV 20P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    15                128
  RECTAL MUCINOUS ADENOCARCINOMA            2                 11
D72V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          0   18
  20P LOSS WILD-TYPE    6  138
     clus
vv    20P LOSS CNV 20P LOSS WILD-TYPE
  NO             0                  6
  YES           18                138
                    vv
clus                  M0  M1 M1A  MX
  20P LOSS CNV        14   3   0   1
  20P LOSS WILD-TYPE 109  19   2  12
D72V6, multiclass
     clus
vv    20P LOSS CNV 20P LOSS WILD-TYPE
  M0            14                109
  M1             3                 19
  M1A            0                  2
  MX             1                 12
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  20P LOSS CNV       10  4   0   1   0  2   0   1  0
  20P LOSS WILD-TYPE 73 31   4   4   1 21   2   6  1
D72V7, multiclass
                    vv
clus                  R0  R1  R2  RX
  20P LOSS CNV        15   1   2   0
  20P LOSS WILD-TYPE 106   1  10   3
D72V8, multiclass
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  R0           15                106
  R1            1                  1
  R2            2                 10
  RX            0                  3
D72V9, continuous
D72V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P LOSS CNV             1        5         3         0         0         0
  20P LOSS WILD-TYPE      29        3        35         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P LOSS CNV                1          2          2        2         2
  20P LOSS WILD-TYPE          8         21         11       15         7
D72V11, multiclass

Clustering(73) Variable = 21q loss
D73V1, survival
                    sevent
clus2                 0  1
  21Q LOSS CNV       30  3
  21Q LOSS WILD-TYPE 89  8
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                33                 97 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 3                  8 
$`21Q LOSS CNV`
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-3575 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-A01L TCGA-AG-A01N 
       12.00         1.02         1.02         0.99        12.00        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CL-4957 
       63.98        10.98        61.94        40.96         0.69        13.97 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        7.36         6.97       119.51        57.24       121.08        51.48 
TCGA-DY-A1H8 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-7002 
       32.58         2.17         3.98         0.66         6.90         2.76 
TCGA-EI-7004 TCGA-F5-6810 TCGA-F5-6863 
        2.04         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-3586 TCGA-AG-3605 
       10.39         8.45         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-3883 
        7.96         0.95         1.02         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         0.99        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        1.02         1.02        70.03        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.93        38.01         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.02         6.02         6.94         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.70        60.00         7.99        10.98        11.01         9.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98         6.97        27.91        19.99         5.92 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 
        3.98         5.00         0.26        41.33        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 
        2.40         7.63         0.16         8.22         0.46         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-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        3.39         0.85         2.17         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.08         0.46        18.25        47.70        47.08 
TCGA-G5-6641 
       20.91 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              0.39               0.16 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
            121.08              70.03 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              7.59               5.23 
[1] "0.4 - 121.1 (7.6)" "0.2 - 70.0 (5.2)" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        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 CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "21Q LOSS CNV"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"21Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        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 CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "21Q LOSS CNV"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"21Q LOSS WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        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 CNV" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
      "21Q LOSS CNV"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
      "21Q LOSS CNV"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
"21Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV         22   21
  21Q LOSS WILD-TYPE   52   67
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  FEMALE           22                 52
  MALE             21                 67
D73V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV         38    2
  21Q LOSS WILD-TYPE  105   11
                                clus
vv                               21Q LOSS CNV 21Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    38                105
  RECTAL MUCINOUS ADENOCARCINOMA            2                 11
D73V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          2   41
  21Q LOSS WILD-TYPE    4  115
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  NO             2                  4
  YES           41                115
                    vv
clus                 M0 M1 M1A MX
  21Q LOSS CNV       34  6   0  3
  21Q LOSS WILD-TYPE 89 16   2 10
D73V6, multiclass
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  M0            34                 89
  M1             6                 16
  M1A            0                  2
  MX             3                 10
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  21Q LOSS CNV       16 14   1   2   0  6   0   4  0
  21Q LOSS WILD-TYPE 67 21   3   3   1 17   2   3  1
D73V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS CNV       31  0  3  0
  21Q LOSS WILD-TYPE 90  2  9  3
D73V8, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  R0           31                 90
  R1            0                  2
  R2            3                  9
  RX            0                  3
D73V9, continuous
D73V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q LOSS CNV             5        3         7         0         0         2
  21Q LOSS WILD-TYPE      25        5        31         2         2         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q LOSS CNV                4         10          2        6         3
  21Q LOSS WILD-TYPE          5         13         11       11         6
D73V11, multiclass

Clustering(74) Variable = 22q loss
D74V1, survival
                    sevent
clus2                 0  1
  22Q LOSS CNV       25  4
  22Q LOSS WILD-TYPE 94  7
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                29                101 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 4                  7 
$`22Q LOSS CNV`
TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       13.55         7.59         7.33        12.00         1.02         2.01 
TCGA-AG-3883 TCGA-AG-3999 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
        1.02         1.02        12.00        10.98         1.94        38.93 
TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 
        0.49         0.72        10.19        13.97         7.36         6.97 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 
       19.99         3.98         5.00        41.33        51.48         2.40 
TCGA-EI-6881 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6641 
        6.15         0.39         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-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        1.02         0.99         0.99         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
        0.99         1.02         1.02         1.02         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.94        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-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-A02N TCGA-AG-A02X TCGA-AG-A032 
       63.98        51.98        49.94        61.94        40.96        38.01 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         4.60         1.81         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-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.92         0.26       119.51        57.24       121.08        24.13 
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-6514 TCGA-EI-6882 
        0.46         3.98         0.66         6.90         7.10         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-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        3.39         0.85         2.17         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.08         0.46        18.25        47.70        47.08 

      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              0.39               0.16 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             51.48             121.08 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              6.97               6.02 
[1] "0.4 - 51.5 (7.0)"  "0.2 - 121.1 (6.0)"
        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 CNV" "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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
      "22Q LOSS CNV" 
        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 CNV" "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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
      "22Q LOSS CNV" 
        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 CNV" "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 CNV" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3575 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3599 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3726         TCGA-AG-3727 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3742         TCGA-AG-3878 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3887         TCGA-AG-3892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4007 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4022         TCGA-AG-A002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01N         TCGA-AG-A01W 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A023 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV"       "22Q LOSS CNV" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AH-6644         TCGA-AH-6897         TCGA-AH-6903 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BM-6198         TCGA-CI-6619         TCGA-CI-6620 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CL-4957         TCGA-CL-5917         TCGA-CL-5918 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-4745         TCGA-DC-4749         TCGA-DC-5337 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6154         TCGA-DC-6155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6156         TCGA-DC-6157         TCGA-DC-6158 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6465         TCGA-F5-6571 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6810         TCGA-F5-6811 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-F5-6814 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-F5-6861         TCGA-F5-6863         TCGA-F5-6864 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6233         TCGA-G5-6235         TCGA-G5-6572 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G5-6641 
      "22Q LOSS CNV" 
[1] "hr=" "4.1"
D74V2, continuous
D74V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV         17   25
  22Q LOSS WILD-TYPE   57   63
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  FEMALE           17                 57
  MALE             25                 63
D74V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV         37    4
  22Q LOSS WILD-TYPE  106    9
                                clus
vv                               22Q LOSS CNV 22Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    37                106
  RECTAL MUCINOUS ADENOCARCINOMA            4                  9
D74V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          3   39
  22Q LOSS WILD-TYPE    3  117
     clus
vv    22Q LOSS CNV 22Q LOSS WILD-TYPE
  NO             3                  3
  YES           39                117
                    vv
clus                 M0 M1 M1A MX
  22Q LOSS CNV       30  6   0  5
  22Q LOSS WILD-TYPE 93 16   2  8
D74V6, multiclass
     clus
vv    22Q LOSS CNV 22Q LOSS WILD-TYPE
  M0            30                 93
  M1             6                 16
  M1A            0                  2
  MX             5                  8
                    vv
clus                 N0 N1 N1A N1B N1C N2 N2A N2B NX
  22Q LOSS CNV       17 14   0   3   0  6   0   1  1
  22Q LOSS WILD-TYPE 66 21   4   2   1 17   2   6  0
D74V7, multiclass
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS CNV       30  1  3  0
  22Q LOSS WILD-TYPE 91  1  9  3
D74V8, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  R0           30                 91
  R1            1                  1
  R2            3                  9
  RX            0                  3
D74V9, continuous
D74V10, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q LOSS CNV             4        2        11         0         0         3
  22Q LOSS WILD-TYPE      26        6        27         2         2         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q LOSS CNV                4          8          2        5         1
  22Q LOSS WILD-TYPE          5         15         11       12         8
D74V11, multiclass

Clustering(75) Variable = Xq loss
D75V1, survival
                   sevent
clus2                 0   1
  XQ LOSS CNV         3   0
  XQ LOSS WILD-TYPE 116  11
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               127 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                0                11 
$`XQ LOSS CNV`
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-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
        7.33        12.00         1.02         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        1.02         0.99         0.99         7.96         0.95         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02         0.92         1.02         0.99 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         1.02         1.02         1.02         1.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        0.99        20.94        13.91         6.02        25.94        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.91        13.02         1.02         1.02        12.00        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        63.98        10.98        51.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.93        61.94        38.01         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.02         6.02 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.94         9.37         4.70        13.97        60.00         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01         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 

      XQ LOSS CNV XQ LOSS WILD-TYPE 
            19.10              0.16 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            40.96            121.08 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            23.01              6.02 
[1] "19.1 - 41.0 (23.0)" "0.2 - 121.1 (6.0)" 
       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 CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AG-3575        TCGA-AG-3581 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3586        TCGA-AG-3587 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3599        TCGA-AG-3605        TCGA-AG-3726        TCGA-AG-3727 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3742        TCGA-AG-3878        TCGA-AG-3883 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-4022        TCGA-AG-A002        TCGA-AG-A008 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01J 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01N        TCGA-AG-A01W        TCGA-AG-A01Y 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A023        TCGA-AG-A025        TCGA-AG-A026 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AH-6897        TCGA-AH-6903        TCGA-BM-6198        TCGA-CI-6619 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CI-6620        TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CL-4957        TCGA-CL-5917        TCGA-CL-5918        TCGA-DC-4745 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-4749        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6154 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6155        TCGA-DC-6156        TCGA-DC-6157        TCGA-DC-6158 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682        TCGA-DC-6683 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6465 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810        TCGA-F5-6811 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814        TCGA-F5-6861 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233        TCGA-G5-6235 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G5-6572        TCGA-G5-6641 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D75V2, continuous
D75V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          2    4
  XQ LOSS WILD-TYPE   72   84
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  FEMALE           2                72
  MALE             4                84
D75V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          5    0
  XQ LOSS WILD-TYPE  138   13
                                clus
vv                               XQ LOSS CNV XQ LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                    5               138
  RECTAL MUCINOUS ADENOCARCINOMA           0                13
D75V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          0    6
  XQ LOSS WILD-TYPE    6  150
     clus
vv    XQ LOSS CNV XQ LOSS WILD-TYPE
  NO            0                 6
  YES           6               150
                   vv
clus                 M0  M1 M1A  MX
  XQ LOSS CNV         3   2   0   1
  XQ LOSS WILD-TYPE 120  20   2  12
D75V6, multiclass
     clus
vv    XQ LOSS CNV XQ LOSS WILD-TYPE
  M0            3               120
  M1            2                20
  M1A           0                 2
  MX            1                12
                   vv
clus                N0 N1 N1A N1B N1C N2 N2A N2B NX
  XQ LOSS CNV        4  0   0   0   0  2   0   0  0
  XQ LOSS WILD-TYPE 79 35   4   5   1 21   2   7  1
D75V7, multiclass
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS CNV         3   0   2   0
  XQ LOSS WILD-TYPE 118   2  10   3
D75V8, multiclass
    clus
vv   XQ LOSS CNV XQ LOSS WILD-TYPE
  R0           3               118
  R1           0                 2
  R2           2                10
  RX           0                 3
D75V9, continuous
D75V10, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ LOSS CNV             2        0         2         0         0         0
  XQ LOSS WILD-TYPE      28        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ LOSS CNV                0          0          0        2         0
  XQ LOSS WILD-TYPE          9         23         13       15         9
D75V11, multiclass
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
                                "GENDER" 
                                      V4 
                     "HISTOLOGICAL.TYPE" 
                                      V5 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V6 
                    "DISTANT.METASTASIS" 
                                      V7 
                 "LYMPH.NODE.METASTASIS" 
                                      V8 
             "COMPLETENESS.OF.RESECTION" 
                                      V9 
                 "NUMBER.OF.LYMPH.NODES" 
                                     V10 
                       "TUMOR.STAGECODE" 
                                     V11 
                 "NEOPLASM.DISEASESTAGE" 
> q(save="no")
