
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/CESC-TP/3472492/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/CESC-TP/3349247/CESC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC-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=CESC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=50, in cluster file=126, common to both=42
[1] "Reduce the number of clustering variables from 80 to 49."
[1] 49 42
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                9                33 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                9                33 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               16                26 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               16                26 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
                5                37 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                5                37 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                5                37 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                5                37 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               25                17 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               25                17 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               11                31 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               11                31 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                8                34 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                8                34 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                39 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                39 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                4                38 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                4                38 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                38 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                38 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                35 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                35 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 3                 39 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 3                 39 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 6                 36 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 6                 36 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 4                 38 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 4                 38 
[1] "14q gain"
[1] 3
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                 38 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                 38 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 3                 39 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 3                 39 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 5                 37 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 5                 37 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                 38 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 4                 38 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 38 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 38 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 39 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 39 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 8                 34 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 8                 34 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 29 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 29 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                14                 28 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                14                 28 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                 39 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                 39 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                 37 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                 37 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
               11                31 
      3P LOSS CNV 3P LOSS WILD-TYPE 
               11                31 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
               15                27 
      4P LOSS CNV 4P LOSS WILD-TYPE 
               15                27 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                5                37 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                5                37 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               11                31 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               11                31 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                3                39 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                3                39 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                5                37 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                5                37 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                4                38 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                4                38 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                4                38 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                4                38 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               11                31 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               11                31 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                38 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                38 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                3                39 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                3                39 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                 35 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 7                 35 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 7                 35 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 7                 35 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 9                 33 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 9                 33 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                10                 32 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                10                 32 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 7                 35 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 7                 35 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 33 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 33 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                10                 32 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                10                 32 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 39 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 39 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 7                 35 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 7                 35 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 8                 34 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 8                 34 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                 38 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                 38 
[1] "20p loss"
[1] 3
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 3                 39 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 3                 39 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 6                 36 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 6                 36 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 42 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
        1505          925         1112         5385           NA           NA 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
        1616           NA           NA           NA         2382         2155 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
        1289           NA           81         2127         2892          183 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 
           8           53           40           25           19           20 
TCGA-EA-A43B TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K 
          54           NA          178          241          211           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
          37           30           66            2           31           44 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
          48           24          106          773           NA          168 
Variable 1:'AGE':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=34,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "NUMBER.OF.LYMPH.NODES"                 
[7] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T1B T1B1 T1B2  T2A T2A1 T2A2  T2B  T3B 
   6   14    4    2    3    2    6    1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 42 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=30, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=4, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1p gain
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN CNV        8  1
  1P GAIN WILD-TYPE 26  6
      1P GAIN CNV 1P GAIN WILD-TYPE 
                9                32 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1                 6 
$`1P GAIN CNV`
TCGA-C5-A1BK TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A439 
      177.04         2.43        70.85         1.74         0.62         0.66 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-HM-A3JK 
        1.45         1.58         5.52 

$`1P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       35.61        40.93        78.31        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93        95.08         6.02         0.26         1.32         0.82 
TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        1.78         5.85         7.92         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.99         2.17         0.07         1.02         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ 
       25.41        21.67 

      1P GAIN CNV 1P GAIN WILD-TYPE 
             0.62              0.07 
      1P GAIN CNV 1P GAIN WILD-TYPE 
           177.04             95.08 
      1P GAIN CNV 1P GAIN WILD-TYPE 
             1.74              6.48 
[1] "0.6 - 177.0 (1.7)" "0.1 - 95.1 (6.5)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1P GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1P GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1P GAIN CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1P GAIN CNV" 
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          2    7
  1P GAIN WILD-TYPE   11   22
     clus
vv    1P GAIN CNV 1P GAIN WILD-TYPE
  NO            2                11
  YES           7                22
D1V4, continuous
[1] "Remove cluster labels:" "1P GAIN CNV"           
clus
      1P GAIN CNV 1P GAIN WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-C5-A1MI        TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3WB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3YQ 
"1P GAIN WILD-TYPE" 
D1V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          4    4
  1P GAIN WILD-TYPE   19   10
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  M0           4                19
  MX           4                10
D1V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          5    3
  1P GAIN WILD-TYPE   19   11
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  N0           5                19
  N1           3                11
D1V7, continuous
D1V8, continuous

Clustering(2) Variable = 1q gain
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN CNV       13  2
  1Q GAIN WILD-TYPE 21  5
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               15                26 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                2                 5 
$`1Q GAIN CNV`
TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL 
      177.04         5.46        53.13         2.43        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EA-A439 TCGA-FU-A23L 
       42.38         6.02         1.74         0.62         0.66         1.22 
TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JK 
        2.17         1.45         5.52 

$`1Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1M5 TCGA-C5-A1MI TCGA-C5-A1MN 
       49.48        30.41        36.56        67.46        35.61        40.93 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR 
       36.76         2.66        69.93        95.08         0.26         1.32 
TCGA-EA-A3HS TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K 
        0.82         1.78         5.85         7.92         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.99         0.07         1.02         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ 
       25.41        21.67 

      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             0.62              0.07 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
           177.04             95.08 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
            5.460             6.395 
[1] "0.6 - 177.0 (5.5)" "0.1 - 95.1 (6.4)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1Q GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1Q GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
      "1Q GAIN CNV" 
[1] "hr=" "1.8"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          7    9
  1Q GAIN WILD-TYPE    6   20
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  NO            7                 6
  YES           9                20
D2V4, continuous
D2V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          7    6
  1Q GAIN WILD-TYPE   16    8
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  M0           7                16
  MX           6                 8
D2V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          9    4
  1Q GAIN WILD-TYPE   15   10
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  N0           9                15
  N1           4                10
D2V7, continuous
D2V8, continuous

Clustering(3) Variable = 2p gain
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN CNV        4  1
  2P GAIN WILD-TYPE 30  6
      2P GAIN CNV 2P GAIN WILD-TYPE 
                5                36 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                1                 6 
$`2P GAIN CNV`
TCGA-C5-A1BN TCGA-DS-A3LQ TCGA-EA-A439 TCGA-EX-A1H6 TCGA-FU-A23L 
        5.46         6.02         0.66         7.92         1.22 

$`2P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56       177.04        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.32         0.82         0.62         1.78         5.85         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        1.22         0.99         2.17         0.07         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.58         0.79         3.48        25.41        21.67         5.52 

      2P GAIN CNV 2P GAIN WILD-TYPE 
             0.66              0.07 
      2P GAIN CNV 2P GAIN WILD-TYPE 
             7.92            177.04 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            5.460             5.685 
[1] "0.7 - 7.9 (5.5)"   "0.1 - 177.0 (5.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"2P GAIN WILD-TYPE" 
[1] "hr=" "6.8"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          2    3
  2P GAIN WILD-TYPE   11   26
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  NO            2                11
  YES           3                26
D3V4, continuous
[1] "Remove cluster labels:" "2P GAIN CNV"           
clus
      2P GAIN CNV 2P GAIN WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1MF        TCGA-C5-A1MI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FU-A3YQ 
"2P GAIN WILD-TYPE" 
D3V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          2    2
  2P GAIN WILD-TYPE   21   12
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  M0           2                21
  MX           2                12
D3V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          3    1
  2P GAIN WILD-TYPE   21   13
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  N0           3                21
  N1           1                13
D3V7, continuous
D3V8, continuous

Clustering(4) Variable = 3p gain
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN CNV        4  1
  3P GAIN WILD-TYPE 30  6
      3P GAIN CNV 3P GAIN WILD-TYPE 
                5                36 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                 6 
$`3P GAIN CNV`
TCGA-DS-A0VL TCGA-EA-A439 TCGA-FU-A3NI TCGA-HM-A3JJ TCGA-HM-A3JK 
        2.66         0.66         1.45        21.67         5.52 

$`3P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
       42.38        36.76        69.93        95.08         6.02         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 
        1.74         1.32         0.82         0.62         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.02         1.58         0.79         3.48        25.41 

      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.66              0.07 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            21.67            177.04 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            2.660             5.935 
[1] "0.7 - 21.7 (2.7)"  "0.1 - 177.0 (5.9)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-HM-A3JK 
      "3P GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-HM-A3JK 
      "3P GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-HM-A3JK 
      "3P GAIN CNV" 
[1] "hr=" "5.1"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          2    3
  3P GAIN WILD-TYPE   11   26
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  NO            2                11
  YES           3                26
D4V4, continuous
D4V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          2    3
  3P GAIN WILD-TYPE   21   11
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  M0           2                21
  MX           3                11
D4V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          2    3
  3P GAIN WILD-TYPE   22   11
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  N0           2                22
  N1           3                11
D4V7, continuous
D4V8, continuous

Clustering(5) Variable = 3q gain
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN CNV       20  4
  3Q GAIN WILD-TYPE 14  3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               24                17 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                4                 3 
$`3Q GAIN CNV`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        36.56       177.04        67.46        53.13         2.43 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       78.31        70.85        36.76         2.66        69.93        95.08 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 
        0.26         1.74         1.32         0.82         0.62         0.66 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB TCGA-HM-A3JJ TCGA-HM-A3JK 
        5.85         1.22         1.45         0.79        21.67         5.52 

$`3Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DR-A0ZM TCGA-DS-A3LQ 
       30.41         5.46        35.61        40.93        42.38         6.02 
TCGA-EA-A43B TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        1.78         7.92         6.94         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.02         1.58         3.48        25.41 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
             0.26              0.07 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
           177.04             42.38 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            5.685             5.460 
[1] "0.3 - 177.0 (5.7)" "0.1 - 42.4 (5.5)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-HM-A3JK 
      "3Q GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-HM-A3JK 
      "3Q GAIN CNV" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-HM-A3JK 
      "3Q GAIN CNV" 
[1] "hr=" "2.6"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          8   17
  3Q GAIN WILD-TYPE    5   12
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  NO            8                 5
  YES          17                12
D5V4, continuous
D5V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV         15    8
  3Q GAIN WILD-TYPE    8    6
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  M0          15                 8
  MX           8                 6
D5V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV         15    8
  3Q GAIN WILD-TYPE    9    6
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  N0          15                 9
  N1           8                 6
D5V7, continuous
D5V8, continuous

Clustering(6) Variable = 5p gain
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN CNV        8  2
  5P GAIN WILD-TYPE 26  5
      5P GAIN CNV 5P GAIN WILD-TYPE 
               10                31 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                2                 5 
$`5P GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1MN TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EA-A439 TCGA-EA-A43B 
       30.41        40.93         6.02         1.32         0.66         1.78 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI TCGA-HM-A3JJ 
        5.85         1.22         1.45        21.67 

$`5P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
        2.66        69.93        95.08         0.26         1.74         0.82 
TCGA-EA-A3HT TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62         7.92         6.94         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.02         1.58         0.79         3.48        25.41 
TCGA-HM-A3JK 
        5.52 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             0.66              0.07 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            40.93            177.04 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            3.815             5.520 
[1] "0.7 - 40.9 (3.8)"  "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" 
[1] "hr=" "3"  
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          4    7
  5P GAIN WILD-TYPE    9   22
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  NO            4                 9
  YES           7                22
D6V4, continuous
[1] "Remove cluster labels:" "5P GAIN CNV"           
clus
      5P GAIN CNV 5P GAIN WILD-TYPE 
                2                12 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-C5-A1MI        TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D6V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          5    4
  5P GAIN WILD-TYPE   18   10
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  M0           5                18
  MX           4                10
D6V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          5    4
  5P GAIN WILD-TYPE   19   10
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  N0           5                19
  N1           4                10
D6V7, continuous
D6V8, continuous

Clustering(7) Variable = 6p gain
D7V1, survival
                   sevent
clus2                0  1
  6P GAIN CNV        6  2
  6P GAIN WILD-TYPE 28  5
      6P GAIN CNV 6P GAIN WILD-TYPE 
                8                33 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                 5 
$`6P GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A2LY TCGA-EA-A439 TCGA-EA-A43B 
       30.41         5.46        35.61        78.31         0.66         1.78 
TCGA-FU-A23K TCGA-FU-A23L 
        1.22         1.22 

$`6P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        36.56       177.04        67.46        53.13         2.43 
TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       95.08         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62         5.85         7.92         6.94         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       25.41        21.67         5.52 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             0.66              0.07 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            78.31            177.04 
      6P GAIN CNV 6P GAIN WILD-TYPE 
             3.62              5.85 
[1] "0.7 - 78.3 (3.6)"  "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          3    5
  6P GAIN WILD-TYPE   10   24
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  NO            3                10
  YES           5                24
D7V4, continuous
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                12 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1MF        TCGA-C5-A1MN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D7V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          5    2
  6P GAIN WILD-TYPE   18   12
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  M0           5                18
  MX           2                12
D7V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          5    2
  6P GAIN WILD-TYPE   19   12
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  N0           5                19
  N1           2                12
D7V7, continuous
D7V8, continuous

Clustering(8) Variable = 6q gain
D8V1, survival
                   sevent
clus2                0  1
  6Q GAIN CNV        2  1
  6Q GAIN WILD-TYPE 32  6
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                38 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1                 6 
$`6Q GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-EA-A439 
       30.41        35.61         0.66 

$`6Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.32         0.82         0.62         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             0.66              0.07 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            35.61            177.04 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            30.41              5.49 
[1] "0.7 - 35.6 (30.4)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q GAIN WILD-TYPE" 
[1] "hr=" "3.3"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          1    2
  6Q GAIN WILD-TYPE   12   27
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  NO            1                12
  YES           2                27
D8V4, continuous
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3YQ 
"6Q GAIN WILD-TYPE" 
D8V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          3    0
  6Q GAIN WILD-TYPE   20   14
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  M0           3                20
  MX           0                14
D8V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          2    1
  6Q GAIN WILD-TYPE   22   13
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  N0           2                22
  N1           1                13
D8V7, continuous
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                34 
       TCGA-BI-A0VR        TCGA-C5-A1BK        TCGA-C5-A1M5        TCGA-C5-A1MF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-C5-A2LY        TCGA-DR-A0ZL        TCGA-DR-A0ZM        TCGA-DS-A0VK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN        TCGA-DS-A3LQ 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR        TCGA-EA-A3HS 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EA-A3HT        TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HM-A3JJ        TCGA-HM-A3JK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D8V8, continuous

Clustering(9) Variable = 7q gain
D9V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV        4  0
  7Q GAIN WILD-TYPE 30  7
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                4                37 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                0                 7 
$`7Q GAIN CNV`
TCGA-C5-A1MF TCGA-C5-A2LY TCGA-DS-A3LQ TCGA-FU-A3NI 
       53.13        78.31         6.02         1.45 

$`7Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        40.93        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.02         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             1.45              0.07 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            78.31            177.04 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
           29.575             5.460 
[1] "1.4 - 78.3 (29.6)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q GAIN WILD-TYPE" 
[1] "hr="     "2.4e+08"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          3    1
  7Q GAIN WILD-TYPE   10   28
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  NO            3                10
  YES           1                28
D9V4, continuous
[1] "Remove cluster labels:" "7Q GAIN CNV"           
clus
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MI 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FU-A3YQ 
"7Q GAIN WILD-TYPE" 
D9V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          2    2
  7Q GAIN WILD-TYPE   21   12
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0           2                21
  MX           2                12
D9V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          2    2
  7Q GAIN WILD-TYPE   22   12
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  N0           2                22
  N1           2                12
D9V7, continuous
D9V8, continuous

Clustering(10) Variable = 8p gain
D10V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV        3  1
  8P GAIN WILD-TYPE 31  6
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                37 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                1                 6 
$`8P GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46         6.02         1.74 

$`8P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        36.56       177.04         5.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66        69.93        95.08         0.26         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.62         0.66         1.78         5.85         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             1.74              0.07 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            67.46            177.04 
      8P GAIN CNV 8P GAIN WILD-TYPE 
           18.215             5.460 
[1] "1.7 - 67.5 (18.2)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          1    3
  8P GAIN WILD-TYPE   12   26
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  NO            1                12
  YES           3                26
D10V4, continuous
D10V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          4    0
  8P GAIN WILD-TYPE   19   14
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  M0           4                19
  MX           0                14
D10V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          3    1
  8P GAIN WILD-TYPE   21   13
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  N0           3                21
  N1           1                13
D10V7, continuous
D10V8, continuous

Clustering(11) Variable = 8q gain
D11V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV        6  1
  8Q GAIN WILD-TYPE 28  6
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                34 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                1                 6 
$`8Q GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46        53.13        69.93         6.02         1.74 
TCGA-FU-A3NI 
        1.45 

$`8Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MI TCGA-C5-A1MK 
       49.48        36.56       177.04         5.46        35.61         2.43 
TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       40.93        78.31        70.85        42.38        36.76         2.66 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 
       95.08         0.26         1.32         0.82         0.62         0.66 
TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        1.78         5.85         7.92         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB 
        0.99         2.17         0.07         1.02         1.58         0.79 
TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.48        25.41        21.67         5.52 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             1.45              0.07 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            69.93            177.04 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            30.41              4.47 
[1] "1.4 - 69.9 (30.4)" "0.1 - 177.0 (4.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          2    5
  8Q GAIN WILD-TYPE   11   24
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  NO            2                11
  YES           5                24
D11V4, continuous
[1] "Remove cluster labels:" "8Q GAIN CNV"           
clus
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MI 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3YQ 
"8Q GAIN WILD-TYPE" 
D11V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          5    2
  8Q GAIN WILD-TYPE   18   12
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0           5                18
  MX           2                12
D11V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          4    3
  8Q GAIN WILD-TYPE   20   11
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  N0           4                20
  N1           3                11
D11V7, continuous
D11V8, continuous

Clustering(12) Variable = 10p gain
D12V1, survival
                    sevent
clus2                 0  1
  10P GAIN CNV        2  1
  10P GAIN WILD-TYPE 32  6
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 3                 38 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 1                  6 
$`10P GAIN CNV`
TCGA-BI-A0VS TCGA-DS-A0VK TCGA-FU-A3NI 
       30.41        36.76         1.45 

$`10P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 
        1.32         0.82         0.62         0.66         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.07         1.02         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      10P GAIN CNV 10P GAIN WILD-TYPE 
              1.45               0.07 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             36.76             177.04 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             30.41               5.49 
[1] "1.4 - 36.8 (30.4)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          0    3
  10P GAIN WILD-TYPE   13   26
     clus
vv    10P GAIN CNV 10P GAIN WILD-TYPE
  NO             0                 13
  YES            3                 26
D12V4, continuous
D12V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          2    1
  10P GAIN WILD-TYPE   21   13
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  M0            2                 21
  MX            1                 13
D12V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          1    2
  10P GAIN WILD-TYPE   23   12
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  N0            1                 23
  N1            2                 12
D12V7, continuous
D12V8, continuous

Clustering(13) Variable = 12p gain
D13V1, survival
                    sevent
clus2                 0  1
  12P GAIN CNV        6  0
  12P GAIN WILD-TYPE 28  7
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 6                 35 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 0                  7 
$`12P GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1MF TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       30.41        53.13         6.02         1.22         2.17         1.45 

$`12P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MI 
       49.48        36.56       177.04         5.46        67.46        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        6.94         1.22         0.99         0.07         1.02         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.79         3.48        25.41        21.67         5.52 

      12P GAIN CNV 12P GAIN WILD-TYPE 
              1.22               0.07 
      12P GAIN CNV 12P GAIN WILD-TYPE 
             53.13             177.04 
      12P GAIN CNV 12P GAIN WILD-TYPE 
             4.095              5.520 
[1] "1.2 - 53.1 (4.1)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr="     "7.9e+07"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          2    4
  12P GAIN WILD-TYPE   11   25
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  NO             2                 11
  YES            4                 25
D13V4, continuous
[1] "Remove cluster labels:" "12P GAIN CNV"          
clus
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 2                 12 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MN         TCGA-DR-A0ZM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D13V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          2    4
  12P GAIN WILD-TYPE   21   10
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  M0            2                 21
  MX            4                 10
D13V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          4    2
  12P GAIN WILD-TYPE   20   12
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  N0            4                 20
  N1            2                 12
D13V7, continuous
D13V8, continuous

Clustering(14) Variable = 12q gain
D14V1, survival
                    sevent
clus2                 0  1
  12Q GAIN CNV        4  0
  12Q GAIN WILD-TYPE 30  7
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 4                 37 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 0                  7 
$`12Q GAIN CNV`
TCGA-C5-A1MF TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3NI 
       53.13         6.02         1.22         1.45 

$`12Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 
        1.32         0.82         0.62         0.66         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        7.92         6.94         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.02         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              1.22               0.07 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             53.13             177.04 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             3.735              5.520 
[1] "1.2 - 53.1 (3.7)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          2    2
  12Q GAIN WILD-TYPE   11   27
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  NO             2                 11
  YES            2                 27
D14V4, continuous
[1] "Remove cluster labels:" "12Q GAIN CNV"          
clus
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 1                 13 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-C5-A1MI         TCGA-C5-A1MN         TCGA-DR-A0ZM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ 
"12Q GAIN WILD-TYPE" 
D14V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          1    3
  12Q GAIN WILD-TYPE   22   11
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0            1                 22
  MX            3                 11
D14V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          2    2
  12Q GAIN WILD-TYPE   22   12
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  N0            2                 22
  N1            2                 12
D14V7, continuous
D14V8, continuous

Clustering(15) Variable = 14q gain
D15V1, survival
                    sevent
clus2                 0  1
  14Q GAIN CNV        3  1
  14Q GAIN WILD-TYPE 31  6
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 4                 37 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 1                  6 
$`14Q GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-EA-A439 TCGA-FU-A3HY 
       30.41        35.61         0.66         0.07 

$`14Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.32         0.82         0.62         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.94         1.22         1.22         0.99         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      14Q GAIN CNV 14Q GAIN WILD-TYPE 
              0.07               0.26 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
             35.61             177.04 
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
            15.535              5.520 
[1] "0.1 - 35.6 (15.5)" "0.3 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"14Q GAIN WILD-TYPE"       "14Q GAIN CNV" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"       "14Q GAIN CNV" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "3.3"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          1    3
  14Q GAIN WILD-TYPE   12   26
     clus
vv    14Q GAIN CNV 14Q GAIN WILD-TYPE
  NO             1                 12
  YES            3                 26
D15V4, continuous
[1] "Remove cluster labels:" "14Q GAIN CNV"          
clus
      14Q GAIN CNV 14Q GAIN WILD-TYPE 
                 2                 12 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MN         TCGA-DR-A0ZM 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D15V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          3    1
  14Q GAIN WILD-TYPE   20   13
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  M0            3                 20
  MX            1                 13
D15V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN CNV          2    2
  14Q GAIN WILD-TYPE   22   12
    clus
vv   14Q GAIN CNV 14Q GAIN WILD-TYPE
  N0            2                 22
  N1            2                 12
D15V7, continuous
D15V8, continuous

Clustering(16) Variable = 15q gain
D16V1, survival
                    sevent
clus2                 0  1
  15Q GAIN CNV        3  0
  15Q GAIN WILD-TYPE 31  7
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 3                 38 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 0                  7 
$`15Q GAIN CNV`
TCGA-EA-A3HQ TCGA-EX-A3L1 TCGA-FU-A23L 
        1.74         6.94         1.22 

$`15Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       42.38        36.76         2.66        69.93        95.08         6.02 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        0.26         1.32         0.82         0.62         0.66         1.78 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        5.85         7.92         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              1.22               0.07 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              6.94             177.04 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             1.740              5.685 
[1] "1.2 - 6.9 (1.7)"   "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "15Q GAIN CNV" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr="     "9500000"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          0    3
  15Q GAIN WILD-TYPE   13   26
     clus
vv    15Q GAIN CNV 15Q GAIN WILD-TYPE
  NO             0                 13
  YES            3                 26
D16V4, continuous
D16V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          2    1
  15Q GAIN WILD-TYPE   21   13
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  M0            2                 21
  MX            1                 13
D16V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          3    0
  15Q GAIN WILD-TYPE   21   14
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  N0            3                 21
  N1            0                 14
D16V7, continuous
D16V8, continuous

Clustering(17) Variable = 16p gain
D17V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV        4  0
  16P GAIN WILD-TYPE 30  7
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 4                 37 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 0                  7 
$`16P GAIN CNV`
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A439 TCGA-FU-A3NI 
        6.02         1.74         0.66         1.45 

$`16P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       42.38        36.76         2.66        69.93        95.08         0.26 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.32         0.82         0.62         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.02         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              0.66               0.07 
      16P GAIN CNV 16P GAIN WILD-TYPE 
              6.02             177.04 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             1.595              5.850 
[1] "0.7 - 6.0 (1.6)"   "0.1 - 177.0 (5.8)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr="     "9500000"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          1    4
  16P GAIN WILD-TYPE   12   25
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  NO             1                 12
  YES            4                 25
D17V4, continuous
D17V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          3    1
  16P GAIN WILD-TYPE   20   13
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  M0            3                 20
  MX            1                 13
D17V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          2    2
  16P GAIN WILD-TYPE   22   12
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  N0            2                 22
  N1            2                 12
D17V7, continuous
D17V8, continuous

Clustering(18) Variable = 16q gain
D18V1, survival
                    sevent
clus2                 0  1
  16Q GAIN CNV        3  0
  16Q GAIN WILD-TYPE 31  7
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 3                 38 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 0                  7 
$`16Q GAIN CNV`
TCGA-DS-A3LQ TCGA-EA-A439 TCGA-EX-A3L1 
        6.02         0.66         6.94 

$`16Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       42.38        36.76         2.66        69.93        95.08         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 
        1.74         1.32         0.82         0.62         1.78         5.85 
TCGA-EX-A1H6 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        7.92         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              0.66               0.07 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              6.94             177.04 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              6.02               5.49 
[1] "0.7 - 6.9 (6.0)"   "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr="     "2.8e+07"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          1    3
  16Q GAIN WILD-TYPE   12   26
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  NO             1                 12
  YES            3                 26
D18V4, continuous
D18V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          3    0
  16Q GAIN WILD-TYPE   20   14
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  M0            3                 20
  MX            0                 14
D18V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          2    1
  16Q GAIN WILD-TYPE   22   13
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  N0            2                 22
  N1            1                 13
D18V7, continuous
[1] "Remove cluster labels:" "16Q GAIN CNV"          
clus
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 2                 34 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A1MI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-HG-A2PA         TCGA-HM-A3JJ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" 
D18V8, continuous

Clustering(19) Variable = 18p gain
D19V1, survival
                    sevent
clus2                 0  1
  18P GAIN CNV        4  0
  18P GAIN WILD-TYPE 30  7
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 37 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 0                  7 
$`18P GAIN CNV`
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-EA-A439 TCGA-HM-A3JK 
       70.85         6.02         0.66         5.52 

$`18P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM 
       53.13        35.61         2.43        40.93        78.31        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        1.32         0.82         0.62         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ 
       21.67 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              0.66               0.07 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             70.85             177.04 
      18P GAIN CNV 18P GAIN WILD-TYPE 
              5.77               5.46 
[1] "0.7 - 70.8 (5.8)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" 
[1] "hr="     "2.2e+08"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          2    2
  18P GAIN WILD-TYPE   11   27
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  NO             2                 11
  YES            2                 27
D19V4, continuous
D19V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          3    1
  18P GAIN WILD-TYPE   20   13
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  M0            3                 20
  MX            1                 13
D19V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          2    2
  18P GAIN WILD-TYPE   22   12
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  N0            2                 22
  N1            2                 12
D19V7, continuous
D19V8, continuous

Clustering(20) Variable = 18q gain
D20V1, survival
                    sevent
clus2                 0  1
  18Q GAIN CNV        3  0
  18Q GAIN WILD-TYPE 31  7
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 3                 38 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 0                  7 
$`18Q GAIN CNV`
TCGA-DS-A3LQ TCGA-EA-A439 TCGA-HM-A3JK 
        6.02         0.66         5.52 

$`18Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT 
       42.38        36.76         2.66        69.93        95.08         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 
        1.74         1.32         0.82         0.62         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ 
       25.41        21.67 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              0.66               0.07 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              6.02             177.04 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             5.520              5.655 
[1] "0.7 - 6.0 (5.5)"   "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
[1] "hr="     "2.8e+07"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          2    1
  18Q GAIN WILD-TYPE   11   28
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  NO             2                 11
  YES            1                 28
D20V4, continuous
D20V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          2    1
  18Q GAIN WILD-TYPE   21   13
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0            2                 21
  MX            1                 13
D20V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    2
  18Q GAIN WILD-TYPE   23   12
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  N0            1                 23
  N1            2                 12
D20V7, continuous
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                 34 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A1MI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-EA-A1QT         TCGA-EA-A3HQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ 
"18Q GAIN WILD-TYPE" 
D20V8, continuous

Clustering(21) Variable = 19q gain
D21V1, survival
                    sevent
clus2                 0  1
  19Q GAIN CNV        5  3
  19Q GAIN WILD-TYPE 29  4
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 8                 33 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 3                  4 
$`19Q GAIN CNV`
TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DS-A3LQ 
        5.46        53.13        35.61         2.43        78.31         6.02 
TCGA-EA-A439 TCGA-EA-A43B 
        0.66         1.78 

$`19Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MN 
       49.48        30.41        36.56       177.04        67.46        40.93 
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       70.85        42.38        36.76         2.66        69.93        95.08 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 
        0.26         1.74         1.32         0.82         0.62         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       25.41        21.67         5.52 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              0.66               0.07 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             78.31             177.04 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              5.74               5.52 
[1] "0.7 - 78.3 (5.7)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          6    2
  19Q GAIN WILD-TYPE    7   27
     clus
vv    19Q GAIN CNV 19Q GAIN WILD-TYPE
  NO             6                  7
  YES            2                 27
D21V4, continuous
D21V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          5    1
  19Q GAIN WILD-TYPE   18   13
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  M0            5                 18
  MX            1                 13
D21V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          4    2
  19Q GAIN WILD-TYPE   20   12
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  N0            4                 20
  N1            2                 12
D21V7, continuous
D21V8, continuous

Clustering(22) Variable = 20p gain
D22V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV        9  4
  20P GAIN WILD-TYPE 25  3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 28 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 4                  3 
$`20P GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41        67.46        35.61        40.93         6.02         1.74 
TCGA-EA-A3HS TCGA-EA-A439 TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JJ 
        0.82         0.66         1.22         2.17         1.45        21.67 
TCGA-HM-A3JK 
        5.52 

$`20P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MK 
       49.48        36.56       177.04         5.46        53.13         2.43 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       78.31        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 
       95.08         0.26         1.32         0.62         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ 
        7.92         6.94         1.22         0.99         0.07         1.02 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.58         0.79         3.48        25.41 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.66               0.07 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             67.46             177.04 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             5.520              5.655 
[1] "0.7 - 67.5 (5.5)"  "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20P GAIN CNV"       "20P GAIN CNV" 
[1] "hr=" "4.3"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          5    8
  20P GAIN WILD-TYPE    8   21
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  NO             5                  8
  YES            8                 21
D22V4, continuous
D22V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          7    5
  20P GAIN WILD-TYPE   16    9
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  M0            7                 16
  MX            5                  9
D22V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          6    6
  20P GAIN WILD-TYPE   18    8
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  N0            6                 18
  N1            6                  8
D22V7, continuous
D22V8, continuous

Clustering(23) Variable = 20q gain
D23V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV       10  4
  20Q GAIN WILD-TYPE 24  3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                14                 27 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 4                  3 
$`20Q GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-EA-A1QT TCGA-EA-A3HQ 
       30.41        35.61         2.43        40.93         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A439 TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3NI 
        1.32         0.82         0.66         1.22         2.17         1.45 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

$`20Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       78.31        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HT TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
       95.08         6.02         0.62         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        6.94         1.22         0.99         0.07         1.02         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.79         3.48        25.41 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.26               0.07 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             40.93             177.04 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             1.955              6.940 
[1] "0.3 - 40.9 (2.0)"  "0.1 - 177.0 (6.9)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
      "20Q GAIN CNV"       "20Q GAIN CNV" 
[1] "hr=" "10" 
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          5    9
  20Q GAIN WILD-TYPE    8   20
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  NO             5                  8
  YES            9                 20
D23V4, continuous
D23V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          7    5
  20Q GAIN WILD-TYPE   16    9
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  M0            7                 16
  MX            5                  9
D23V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          7    5
  20Q GAIN WILD-TYPE   17    9
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  N0            7                 17
  N1            5                  9
D23V7, continuous
D23V8, continuous

Clustering(24) Variable = 21q gain
D24V1, survival
                    sevent
clus2                 0  1
  21Q GAIN CNV        2  1
  21Q GAIN WILD-TYPE 32  6
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 3                 38 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                  6 
$`21Q GAIN CNV`
TCGA-C5-A1MI TCGA-EA-A3HQ TCGA-HM-A3JK 
       35.61         1.74         5.52 

$`21Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       53.13         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
       36.76         2.66        69.93        95.08         6.02         0.26 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 
        1.32         0.82         0.62         0.66         1.78         5.85 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ 
       25.41        21.67 

      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              1.74               0.07 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
             35.61             177.04 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
             5.520              5.655 
[1] "1.7 - 35.6 (5.5)"  "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
[1] "hr=" "4"  
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          2    1
  21Q GAIN WILD-TYPE   11   28
     clus
vv    21Q GAIN CNV 21Q GAIN WILD-TYPE
  NO             2                 11
  YES            1                 28
D24V4, continuous
[1] "Remove cluster labels:" "21Q GAIN CNV"          
clus
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                 13 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MN         TCGA-DR-A0ZM 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A2QG         TCGA-FU-A3EO 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FU-A3YQ 
"21Q GAIN WILD-TYPE" 
D24V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          2    1
  21Q GAIN WILD-TYPE   21   13
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  M0            2                 21
  MX            1                 13
D24V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          1    2
  21Q GAIN WILD-TYPE   23   12
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  N0            1                 23
  N1            2                 12
D24V7, continuous
D24V8, continuous

Clustering(25) Variable = 22q gain
D25V1, survival
                    sevent
clus2                 0  1
  22Q GAIN CNV        4  0
  22Q GAIN WILD-TYPE 30  7
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 4                 37 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 0                  7 
$`22Q GAIN CNV`
TCGA-BI-A0VS TCGA-C5-A2LY TCGA-DS-A3LQ TCGA-FU-A3NI 
       30.41        78.31         6.02         1.45 

$`22Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        40.93        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93        95.08         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.02         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              1.45               0.07 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             78.31             177.04 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
            18.215              5.460 
[1] "1.4 - 78.3 (18.2)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr="     "2.2e+08"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          2    3
  22Q GAIN WILD-TYPE   11   26
     clus
vv    22Q GAIN CNV 22Q GAIN WILD-TYPE
  NO             2                 11
  YES            3                 26
D25V4, continuous
D25V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          3    1
  22Q GAIN WILD-TYPE   20   13
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  M0            3                 20
  MX            1                 13
D25V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          2    2
  22Q GAIN WILD-TYPE   22   12
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  N0            2                 22
  N1            2                 12
D25V7, continuous
D25V8, continuous

Clustering(26) Variable = 3p loss
D26V1, survival
                   sevent
clus2                0  1
  3P LOSS CNV        8  3
  3P LOSS WILD-TYPE 26  4
      3P LOSS CNV 3P LOSS WILD-TYPE 
               11                30 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                3                 4 
$`3P LOSS CNV`
TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM 
       36.56         5.46        40.93        70.85        36.76        69.93 
TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-FU-A3HY TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.82         5.85         0.07         3.48        25.41 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41       177.04        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ 
        2.43        78.31        42.38         2.66        95.08         6.02 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        0.26         1.74         1.32         0.62         0.66         1.78 
TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        7.92         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.02         1.45         1.58         0.79        21.67         5.52 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             0.07              0.26 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            70.85            177.04 
      3P LOSS CNV 3P LOSS WILD-TYPE 
           25.410             2.545 
[1] "0.1 - 70.8 (25.4)" "0.3 - 177.0 (2.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"3P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          4    7
  3P LOSS WILD-TYPE    9   22
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  NO            4                 9
  YES           7                22
D26V4, continuous
D26V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          6    3
  3P LOSS WILD-TYPE   17   11
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  M0           6                17
  MX           3                11
D26V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          4    5
  3P LOSS WILD-TYPE   20    9
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  N0           4                20
  N1           5                 9
D26V7, continuous
D26V8, continuous

Clustering(27) Variable = 4p loss
D27V1, survival
                   sevent
clus2                0  1
  4P LOSS CNV       12  3
  4P LOSS WILD-TYPE 22  4
      4P LOSS CNV 4P LOSS WILD-TYPE 
               15                26 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                3                 4 
$`4P LOSS CNV`
TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DR-A0ZL 
       36.56       177.04         5.46        53.13        35.61        70.85 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 
       36.76         2.66        95.08         1.32         0.82         5.85 
TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        1.22         0.07         1.45 

$`4P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY 
       49.48        30.41        67.46         2.43        40.93        78.31 
TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HT 
       42.38        69.93         6.02         0.26         1.74         0.62 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        0.66         1.78         7.92         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        2.17         1.02         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             0.07              0.26 
      4P LOSS CNV 4P LOSS WILD-TYPE 
           177.04             78.31 
      4P LOSS CNV 4P LOSS WILD-TYPE 
             5.85              4.50 
[1] "0.1 - 177.0 (5.8)" "0.3 - 78.3 (4.5)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "4P LOSS CNV"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          6    9
  4P LOSS WILD-TYPE    7   20
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  NO            6                 7
  YES           9                20
D27V4, continuous
D27V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          8    6
  4P LOSS WILD-TYPE   15    8
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  M0           8                15
  MX           6                 8
D27V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          8    6
  4P LOSS WILD-TYPE   16    8
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  N0           8                16
  N1           6                 8
D27V7, continuous
D27V8, continuous

Clustering(28) Variable = 4q loss
D28V1, survival
                   sevent
clus2                0  1
  4Q LOSS CNV        3  2
  4Q LOSS WILD-TYPE 31  5
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                5                36 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                2                 5 
$`4Q LOSS CNV`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-EX-A1H5 TCGA-FU-A3NI 
        5.46        35.61        70.85         5.85         1.45 

$`4Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56       177.04        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        78.31        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.82         0.62         0.66         1.78         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.58         0.79         3.48        25.41        21.67         5.52 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             1.45              0.07 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            70.85            177.04 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             5.85              4.50 
[1] "1.4 - 70.8 (5.8)"  "0.1 - 177.0 (4.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          3    2
  4Q LOSS WILD-TYPE   10   27
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  NO            3                10
  YES           2                27
D28V4, continuous
D28V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          2    2
  4Q LOSS WILD-TYPE   21   12
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  M0           2                21
  MX           2                12
D28V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          1    3
  4Q LOSS WILD-TYPE   23   11
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  N0           1                23
  N1           3                11
D28V7, continuous
D28V8, continuous

Clustering(29) Variable = 5q loss
D29V1, survival
                   sevent
clus2                0  1
  5Q LOSS CNV        8  3
  5Q LOSS WILD-TYPE 26  4
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
               11                30 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                3                 4 
$`5Q LOSS CNV`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
        5.46        35.61        70.85        36.76         2.66        69.93 
TCGA-EA-A1QT TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-HG-A2PA 
        0.26         1.22         0.99         0.07        25.41 

$`5Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56       177.04        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ 
        2.43        40.93        78.31        42.38        95.08         6.02 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        1.74         1.32         0.82         0.62         0.66         1.78 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ 
        5.85         7.92         6.94         1.22         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.45         1.58         0.79         3.48        21.67         5.52 

      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             0.07              0.62 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            70.85            177.04 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            5.460             5.685 
[1] "0.1 - 70.8 (5.5)"  "0.6 - 177.0 (5.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV"       "5Q LOSS CNV" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          2    9
  5Q LOSS WILD-TYPE   11   20
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  NO            2                11
  YES           9                20
D29V4, continuous
D29V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          7    2
  5Q LOSS WILD-TYPE   16   12
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  M0           7                16
  MX           2                12
D29V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          6    4
  5Q LOSS WILD-TYPE   18   10
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  N0           6                18
  N1           4                10
D29V7, continuous
D29V8, continuous

Clustering(30) Variable = 6p loss
D30V1, survival
                   sevent
clus2                0  1
  6P LOSS CNV        2  1
  6P LOSS WILD-TYPE 32  6
      6P LOSS CNV 6P LOSS WILD-TYPE 
                3                38 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                1                 6 
$`6P LOSS CNV`
TCGA-DS-A0VK TCGA-EX-A1H6 TCGA-FU-A3HY 
       36.76         7.92         0.07 

$`6P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT 
       42.38         2.66        69.93        95.08         6.02         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        1.74         1.32         0.82         0.62         0.66         1.78 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      6P LOSS CNV 6P LOSS WILD-TYPE 
             0.07              0.26 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            36.76            177.04 
      6P LOSS CNV 6P LOSS WILD-TYPE 
             7.92              5.49 
[1] "0.1 - 36.8 (7.9)"  "0.3 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          0    3
  6P LOSS WILD-TYPE   13   26
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  NO            0                13
  YES           3                26
D30V4, continuous
[1] "Remove cluster labels:" "6P LOSS CNV"           
clus
      6P LOSS CNV 6P LOSS WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-C5-A1MI        TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FU-A3YQ 
"6P LOSS WILD-TYPE" 
D30V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          1    2
  6P LOSS WILD-TYPE   22   12
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  M0           1                22
  MX           2                12
D30V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          1    2
  6P LOSS WILD-TYPE   23   12
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  N0           1                23
  N1           2                12
D30V7, continuous
D30V8, continuous

Clustering(31) Variable = 6q loss
D31V1, survival
                   sevent
clus2                0  1
  6Q LOSS CNV        5  0
  6Q LOSS WILD-TYPE 29  7
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                5                36 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                0                 7 
$`6Q LOSS CNV`
TCGA-C5-A1BI TCGA-EA-A1QT TCGA-EX-A1H6 TCGA-FU-A3HY TCGA-FU-A3YQ 
       36.56         0.26         7.92         0.07         3.48 

$`6Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       35.61         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         6.02         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 
        1.32         0.82         0.62         0.66         1.78         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ 
        6.94         1.22         1.22         0.99         2.17         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        1.45         1.58         0.79        25.41        21.67         5.52 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             0.07              0.62 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            36.56            177.04 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            3.480             5.685 
[1] "0.1 - 36.6 (3.5)"  "0.6 - 177.0 (5.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"6Q LOSS WILD-TYPE" 
[1] "hr="     "7.7e+07"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          1    4
  6Q LOSS WILD-TYPE   12   25
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  NO            1                12
  YES           4                25
D31V4, continuous
D31V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          2    3
  6Q LOSS WILD-TYPE   21   11
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           2                21
  MX           3                11
D31V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          3    2
  6Q LOSS WILD-TYPE   21   12
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  N0           3                21
  N1           2                12
D31V7, continuous
D31V8, continuous

Clustering(32) Variable = 7p loss
D32V1, survival
                   sevent
clus2                0  1
  7P LOSS CNV        3  1
  7P LOSS WILD-TYPE 31  6
      7P LOSS CNV 7P LOSS WILD-TYPE 
                4                37 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                1                 6 
$`7P LOSS CNV`
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-EX-A1H5 
       53.13        35.61        70.85         5.85 

$`7P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        78.31        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       69.93        95.08         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.82         0.62         0.66         1.78         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      7P LOSS CNV 7P LOSS WILD-TYPE 
             5.85              0.07 
      7P LOSS CNV 7P LOSS WILD-TYPE 
            70.85            177.04 
      7P LOSS CNV 7P LOSS WILD-TYPE 
            44.37              3.48 
[1] "5.8 - 70.8 (44.4)" "0.1 - 177.0 (3.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV"       "7P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV"       "7P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV"       "7P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"       "7P LOSS CNV" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          3    1
  7P LOSS WILD-TYPE   10   28
     clus
vv    7P LOSS CNV 7P LOSS WILD-TYPE
  NO            3                10
  YES           1                28
D32V4, continuous
D32V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          2    2
  7P LOSS WILD-TYPE   21   12
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  M0           2                21
  MX           2                12
D32V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          2    2
  7P LOSS WILD-TYPE   22   12
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  N0           2                22
  N1           2                12
D32V7, continuous
D32V8, continuous

Clustering(33) Variable = 7q loss
D33V1, survival
                   sevent
clus2                0  1
  7Q LOSS CNV        2  2
  7Q LOSS WILD-TYPE 32  5
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                4                37 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                2                 5 
$`7Q LOSS CNV`
TCGA-C5-A1BN TCGA-C5-A1MI TCGA-EX-A1H5 TCGA-FU-A2QG 
        5.46        35.61         5.85         0.99 

$`7Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56       177.04        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 
        1.32         0.82         0.62         0.66         1.78         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         1.22         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      7Q LOSS CNV 7Q LOSS WILD-TYPE 
             0.99              0.07 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
            35.61            177.04 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
            5.655             5.520 
[1] "1.0 - 35.6 (5.7)"  "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"7Q LOSS WILD-TYPE" 
[1] "hr=" "9.6"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          3    1
  7Q LOSS WILD-TYPE   10   28
     clus
vv    7Q LOSS CNV 7Q LOSS WILD-TYPE
  NO            3                10
  YES           1                28
D33V4, continuous
D33V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          1    1
  7Q LOSS WILD-TYPE   22   13
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  M0           1                22
  MX           1                13
D33V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          1    2
  7Q LOSS WILD-TYPE   23   12
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  N0           1                23
  N1           2                12
D33V7, continuous
D33V8, continuous

Clustering(34) Variable = 8p loss
D34V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV        7  3
  8P LOSS WILD-TYPE 27  4
      8P LOSS CNV 8P LOSS WILD-TYPE 
               10                31 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3                 4 
$`8P LOSS CNV`
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
        2.43        40.93        78.31        36.76        95.08         0.26 
TCGA-EA-A3HR TCGA-FU-A23K TCGA-FU-A3NI TCGA-FU-A3WB 
        1.32         1.22         1.45         0.79 

$`8P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       53.13        35.61        70.85        42.38         2.66        69.93 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        6.02         1.74         0.82         0.62         0.66         1.78 
TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         7.92         6.94         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.07         1.02         1.58         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             0.26              0.07 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            95.08            177.04 
      8P LOSS CNV 8P LOSS WILD-TYPE 
             1.94              5.85 
[1] "0.3 - 95.1 (1.9)"  "0.1 - 177.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" 
[1] "hr=" "2"  
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          4    7
  8P LOSS WILD-TYPE    9   22
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  NO            4                 9
  YES           7                22
D34V4, continuous
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                2                12 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-C5-A1MI        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3YQ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D34V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          5    3
  8P LOSS WILD-TYPE   18   11
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  M0           5                18
  MX           3                11
D34V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          5    3
  8P LOSS WILD-TYPE   19   11
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  N0           5                19
  N1           3                11
D34V7, continuous
D34V8, continuous

Clustering(35) Variable = 9p loss
D35V1, survival
                   sevent
clus2                0  1
  9P LOSS CNV        2  2
  9P LOSS WILD-TYPE 32  5
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                37 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                2                 5 
$`9P LOSS CNV`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-EA-A1QT TCGA-EA-A3HR 
       35.61        40.93         0.26         1.32 

$`9P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       53.13         2.43        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS 
        2.66        69.93        95.08         6.02         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.62         0.66         1.78         5.85         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        1.22         1.22         0.99         2.17         0.07         1.02 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.45         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             0.26              0.07 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            40.93            177.04 
      9P LOSS CNV 9P LOSS WILD-TYPE 
           18.465             5.520 
[1] "0.3 - 40.9 (18.5)" "0.1 - 177.0 (5.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9P LOSS WILD-TYPE" 
[1] "hr=" "4.2"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          2    2
  9P LOSS WILD-TYPE   11   27
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  NO            2                11
  YES           2                27
D35V4, continuous
[1] "Remove cluster labels:" "9P LOSS CNV"           
clus
      9P LOSS CNV 9P LOSS WILD-TYPE 
                2                12 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB        TCGA-FU-A3YQ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
D35V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          3    0
  9P LOSS WILD-TYPE   20   14
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  M0           3                20
  MX           0                14
D35V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          2    1
  9P LOSS WILD-TYPE   22   13
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  N0           2                22
  N1           1                13
D35V7, continuous
D35V8, continuous

Clustering(36) Variable = 9q loss
D36V1, survival
                   sevent
clus2                0  1
  9Q LOSS CNV        2  1
  9Q LOSS WILD-TYPE 32  6
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                3                38 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                1                 6 
$`9Q LOSS CNV`
TCGA-C5-A1MI TCGA-EA-A1QT TCGA-EA-A3HR 
       35.61         0.26         1.32 

$`9Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       53.13         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       36.76         2.66        69.93        95.08         6.02         1.74 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      9Q LOSS CNV 9Q LOSS WILD-TYPE 
             0.26              0.07 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            35.61            177.04 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            1.320             5.685 
[1] "0.3 - 35.6 (1.3)"  "0.1 - 177.0 (5.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-C5-A1BI        TCGA-C5-A1BK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1BN        TCGA-C5-A1M5        TCGA-C5-A1MF        TCGA-C5-A1MI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-C5-A1MK        TCGA-C5-A1MN        TCGA-C5-A2LY        TCGA-DR-A0ZL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DR-A0ZM        TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DS-A0VN        TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A3HR        TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EA-A439 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EA-A43B        TCGA-EX-A1H5        TCGA-EX-A1H6        TCGA-EX-A3L1 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG        TCGA-FU-A3EO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI        TCGA-FU-A3TQ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3WB        TCGA-FU-A3YQ        TCGA-HG-A2PA        TCGA-HM-A3JJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-HM-A3JK 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "5.7"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          1    2
  9Q LOSS WILD-TYPE   12   27
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  NO            1                12
  YES           2                27
D36V4, continuous
[1] "Remove cluster labels:" "9Q LOSS CNV"           
clus
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                1                13 
       TCGA-BI-A0VR        TCGA-C5-A1BI        TCGA-C5-A1BN        TCGA-C5-A1MF 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-C5-A1MN        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A2QG 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3TQ        TCGA-FU-A3WB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FU-A3YQ 
"9Q LOSS WILD-TYPE" 
D36V5, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          3    0
  9Q LOSS WILD-TYPE   20   14
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  M0           3                20
  MX           0                14
D36V6, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          2    1
  9Q LOSS WILD-TYPE   22   13
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  N0           2                22
  N1           1                13
D36V7, continuous
D36V8, continuous

Clustering(37) Variable = 10p loss
D37V1, survival
                    sevent
clus2                 0  1
  10P LOSS CNV        4  2
  10P LOSS WILD-TYPE 30  5
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 35 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                  5 
$`10P LOSS CNV`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-HM-A3JK 
       35.61        40.93         5.85         1.22         0.99         5.52 

$`10P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       53.13         2.43        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 
        1.32         0.82         0.62         0.66         1.78         7.92 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        6.94         1.22         2.17         0.07         1.02         1.45 
TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.58         0.79         3.48        25.41        21.67 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              0.99               0.07 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             40.93             177.04 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             5.685              5.460 
[1] "1.0 - 40.9 (5.7)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" 
[1] "hr=" "3.2"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          4    3
  10P LOSS WILD-TYPE    9   26
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  NO             4                  9
  YES            3                 26
D37V4, continuous
D37V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          1    3
  10P LOSS WILD-TYPE   22   11
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  M0            1                 22
  MX            3                 11
D37V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          1    4
  10P LOSS WILD-TYPE   23   10
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  N0            1                 23
  N1            4                 10
D37V7, continuous
D37V8, continuous

Clustering(38) Variable = 10q loss
D38V1, survival
                    sevent
clus2                 0  1
  10Q LOSS CNV        5  2
  10Q LOSS WILD-TYPE 29  5
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 7                 34 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                  5 
$`10Q LOSS CNV`
TCGA-C5-A1MI TCGA-DS-A0VK TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3TQ 
       35.61        36.76         5.85         1.22         0.99         1.58 
TCGA-HM-A3JK 
        5.52 

$`10Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM 
       53.13         2.43        40.93        78.31        70.85        42.38 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ 
        2.66        69.93        95.08         6.02         0.26         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 
        1.32         0.82         0.62         0.66         1.78         7.92 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
        6.94         1.22         2.17         0.07         1.02         1.45 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        0.79         3.48        25.41        21.67 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              0.99               0.07 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             36.76             177.04 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              5.52               5.74 
[1] "1.0 - 36.8 (5.5)"  "0.1 - 177.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
[1] "hr=" "4.1"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          3    4
  10Q LOSS WILD-TYPE   10   25
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  NO             3                 10
  YES            4                 25
D38V4, continuous
D38V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          2    4
  10Q LOSS WILD-TYPE   21   10
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  M0            2                 21
  MX            4                 10
D38V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          1    6
  10Q LOSS WILD-TYPE   23    8
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  N0            1                 23
  N1            6                  8
D38V7, continuous
D38V8, continuous

Clustering(39) Variable = 11p loss
D39V1, survival
                    sevent
clus2                 0  1
  11P LOSS CNV        8  1
  11P LOSS WILD-TYPE 26  6
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 9                 32 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                  6 
$`11P LOSS CNV`
TCGA-C5-A1BK TCGA-C5-A1MI TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A43B TCGA-EX-A1H5 
      177.04        35.61        70.85        95.08         1.78         5.85 
TCGA-FU-A23L TCGA-FU-A3NI TCGA-FU-A3WB 
        1.22         1.45         0.79 

$`11P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56         5.46        67.46        53.13 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        78.31        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       69.93         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A439 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        0.62         0.66         7.92         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3YQ TCGA-HG-A2PA 
        2.17         0.07         1.02         1.58         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.79               0.07 
      11P LOSS CNV 11P LOSS WILD-TYPE 
            177.04              78.31 
      11P LOSS CNV 11P LOSS WILD-TYPE 
              5.85               5.49 
[1] "0.8 - 177.0 (5.8)" "0.1 - 78.3 (5.5)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          3    6
  11P LOSS WILD-TYPE   10   23
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  NO             3                 10
  YES            6                 23
D39V4, continuous
D39V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          4    5
  11P LOSS WILD-TYPE   19    9
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  M0            4                 19
  MX            5                  9
D39V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          6    3
  11P LOSS WILD-TYPE   18   11
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  N0            6                 18
  N1            3                 11
D39V7, continuous
D39V8, continuous

Clustering(40) Variable = 11q loss
D40V1, survival
                    sevent
clus2                 0  1
  11Q LOSS CNV        8  1
  11Q LOSS WILD-TYPE 26  6
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 9                 32 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 1                  6 
$`11Q LOSS CNV`
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A43B TCGA-EX-A1H5 
       53.13        35.61        95.08         0.26         1.78         5.85 
TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        1.45         1.58         0.79 

$`11Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
        2.43        40.93        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
        2.66        69.93         6.02         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EA-A439 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.62         0.66         7.92         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3YQ TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              0.26               0.07 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             95.08             177.04 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              1.78               5.77 
[1] "0.3 - 95.1 (1.8)"  "0.1 - 177.0 (5.8)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          4    6
  11Q LOSS WILD-TYPE    9   23
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  NO             4                  9
  YES            6                 23
D40V4, continuous
D40V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          4    5
  11Q LOSS WILD-TYPE   19    9
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  M0            4                 19
  MX            5                  9
D40V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          5    4
  11Q LOSS WILD-TYPE   19   10
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  N0            5                 19
  N1            4                 10
D40V7, continuous
D40V8, continuous

Clustering(41) Variable = 12p loss
D41V1, survival
                    sevent
clus2                 0  1
  12P LOSS CNV        5  2
  12P LOSS WILD-TYPE 29  5
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 7                 34 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 2                  5 
$`12P LOSS CNV`
TCGA-C5-A1BK TCGA-C5-A1MN TCGA-DS-A0VK TCGA-DS-A0VL TCGA-EA-A1QT TCGA-EA-A43B 
      177.04        40.93        36.76         2.66         0.26         1.78 
TCGA-FU-A2QG 
        0.99 

$`12P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM 
       35.61         2.43        78.31        70.85        42.38        69.93 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       95.08         6.02         1.74         1.32         0.82         0.62 
TCGA-EA-A439 TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.66         5.85         7.92         6.94         1.22         1.22 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        2.17         0.07         1.02         1.45         1.58         0.79 
TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.48        25.41        21.67         5.52 

      12P LOSS CNV 12P LOSS WILD-TYPE 
              0.26               0.07 
      12P LOSS CNV 12P LOSS WILD-TYPE 
            177.04              95.08 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             2.660              5.685 
[1] "0.3 - 177.0 (2.7)" "0.1 - 95.1 (5.7)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV"       "12P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV"       "12P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV"       "12P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          1    6
  12P LOSS WILD-TYPE   12   23
     clus
vv    12P LOSS CNV 12P LOSS WILD-TYPE
  NO             1                 12
  YES            6                 23
D41V4, continuous
[1] "Remove cluster labels:" "12P LOSS CNV"          
clus
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 2                 12 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-DR-A0ZM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D41V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          4    1
  12P LOSS WILD-TYPE   19   13
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  M0            4                 19
  MX            1                 13
D41V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          5    1
  12P LOSS WILD-TYPE   19   13
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  N0            5                 19
  N1            1                 13
D41V7, continuous
D41V8, continuous

Clustering(42) Variable = 13q loss
D42V1, survival
                    sevent
clus2                 0  1
  13Q LOSS CNV        8  0
  13Q LOSS WILD-TYPE 26  7
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 8                 33 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 0                  7 
$`13Q LOSS CNV`
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
       95.08         6.02         0.26         5.85         1.22         1.45 
TCGA-FU-A3TQ TCGA-HG-A2PA 
        1.58        25.41 

$`13Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A3HQ TCGA-EA-A3HR 
       42.38        36.76         2.66        69.93         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.82         0.62         0.66         1.78         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3WB 
        1.22         0.99         2.17         0.07         1.02         0.79 
TCGA-FU-A3YQ TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.48        21.67         5.52 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              0.26               0.07 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             95.08             177.04 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             3.715              5.520 
[1] "0.3 - 95.1 (3.7)"  "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr="     "2.3e+08"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          3    6
  13Q LOSS WILD-TYPE   10   23
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  NO             3                 10
  YES            6                 23
D42V4, continuous
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                 12 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MN 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-FU-A2QG         TCGA-FU-A3EO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D42V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          4    4
  13Q LOSS WILD-TYPE   19   10
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0            4                 19
  MX            4                 10
D42V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          4    4
  13Q LOSS WILD-TYPE   20   10
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  N0            4                 20
  N1            4                 10
D42V7, continuous
D42V8, continuous

Clustering(43) Variable = 17p loss
D43V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV        6  4
  17P LOSS WILD-TYPE 28  3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                10                 31 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 4                  3 
$`17P LOSS CNV`
TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL 
        5.46        67.46        40.93        70.85        36.76         2.66 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A3NI 
       95.08         0.26         5.85         1.45 

$`17P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41        36.56       177.04        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ 
        2.43        78.31        42.38        69.93         6.02         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H6 
        1.32         0.82         0.62         0.66         1.78         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ 
        1.02         1.58         0.79         3.48        25.41        21.67 
TCGA-HM-A3JK 
        5.52 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              0.26               0.07 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             95.08             177.04 
      17P LOSS CNV 17P LOSS WILD-TYPE 
            21.305              3.480 
[1] "0.3 - 95.1 (21.3)" "0.1 - 177.0 (3.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          4    6
  17P LOSS WILD-TYPE    9   23
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  NO             4                  9
  YES            6                 23
D43V4, continuous
D43V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          6    2
  17P LOSS WILD-TYPE   17   12
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  M0            6                 17
  MX            2                 12
D43V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          5    3
  17P LOSS WILD-TYPE   19   11
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  N0            5                 19
  N1            3                 11
D43V7, continuous
D43V8, continuous

Clustering(44) Variable = 17q loss
D44V1, survival
                    sevent
clus2                 0  1
  17Q LOSS CNV        2  1
  17Q LOSS WILD-TYPE 32  6
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 38 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 1                  6 
$`17Q LOSS CNV`
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
       36.76        95.08         0.26 

$`17Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR 
       42.38         2.66        69.93         6.02         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      17Q LOSS CNV 17Q LOSS WILD-TYPE 
              0.26               0.07 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             95.08             177.04 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             36.76               5.49 
[1] "0.3 - 95.1 (36.8)" "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          1    2
  17Q LOSS WILD-TYPE   12   27
     clus
vv    17Q LOSS CNV 17Q LOSS WILD-TYPE
  NO             1                 12
  YES            2                 27
D44V4, continuous
D44V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          3    0
  17Q LOSS WILD-TYPE   20   14
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  M0            3                 20
  MX            0                 14
D44V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          2    1
  17Q LOSS WILD-TYPE   22   13
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  N0            2                 22
  N1            1                 13
D44V7, continuous
D44V8, continuous

Clustering(45) Variable = 18p loss
D45V1, survival
                    sevent
clus2                 0  1
  18P LOSS CNV        5  2
  18P LOSS WILD-TYPE 29  5
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 7                 34 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 2                  5 
$`18P LOSS CNV`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H6 
       35.61        40.93        78.31        95.08         0.26         7.92 
TCGA-FU-A3EO 
        2.17 

$`18P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       53.13         2.43        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       69.93         6.02         1.74         1.32         0.82         0.62 
TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.66         1.78         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB 
        0.99         0.07         1.02         1.45         1.58         0.79 
TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        3.48        25.41        21.67         5.52 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              0.26               0.07 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             95.08             177.04 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             35.61               4.47 
[1] "0.3 - 95.1 (35.6)" "0.1 - 177.0 (4.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          4    3
  18P LOSS WILD-TYPE    9   26
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  NO             4                  9
  YES            3                 26
D45V4, continuous
D45V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          4    2
  18P LOSS WILD-TYPE   19   12
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  M0            4                 19
  MX            2                 12
D45V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          5    1
  18P LOSS WILD-TYPE   19   13
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  N0            5                 19
  N1            1                 13
D45V7, continuous
D45V8, continuous

Clustering(46) Variable = 18q loss
D46V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV        6  2
  18Q LOSS WILD-TYPE 28  5
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 8                 33 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 2                  5 
$`18Q LOSS CNV`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT 
       35.61        40.93        78.31        70.85        95.08         0.26 
TCGA-EX-A1H6 TCGA-FU-A3EO 
        7.92         2.17 

$`18Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       53.13         2.43        42.38        36.76         2.66        69.93 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 
        6.02         1.74         1.32         0.82         0.62         0.66 
TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        1.78         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       25.41        21.67         5.52 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.26               0.07 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             95.08             177.04 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             38.27               3.48 
[1] "0.3 - 95.1 (38.3)" "0.1 - 177.0 (3.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "18Q LOSS CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          4    4
  18Q LOSS WILD-TYPE    9   25
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  NO             4                  9
  YES            4                 25
D46V4, continuous
D46V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          5    2
  18Q LOSS WILD-TYPE   18   12
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  M0            5                 18
  MX            2                 12
D46V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          6    1
  18Q LOSS WILD-TYPE   18   13
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  N0            6                 18
  N1            1                 13
D46V7, continuous
D46V8, continuous

Clustering(47) Variable = 19p loss
D47V1, survival
                    sevent
clus2                 0  1
  19P LOSS CNV        1  2
  19P LOSS WILD-TYPE 33  5
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 3                 38 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                  5 
$`19P LOSS CNV`
TCGA-C5-A1MI TCGA-C5-A1MN TCGA-DS-A0VN 
       35.61        40.93        95.08 

$`19P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MK TCGA-C5-A2LY TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       53.13         2.43        78.31        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2.66        69.93         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 
        0.82         0.62         0.66         1.78         5.85         7.92 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA 
        1.02         1.45         1.58         0.79         3.48        25.41 
TCGA-HM-A3JJ TCGA-HM-A3JK 
       21.67         5.52 

      19P LOSS CNV 19P LOSS WILD-TYPE 
             35.61               0.07 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             95.08             177.04 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             40.93               4.47 
[1] "35.6 - 95.1 (40.9)" "0.1 - 177.0 (4.5)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          3    1
  19P LOSS WILD-TYPE   10   28
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  NO             3                 10
  YES            1                 28
D47V4, continuous
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                 12 
        TCGA-BI-A0VR         TCGA-C5-A1BI         TCGA-C5-A1BN 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D47V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          2    0
  19P LOSS WILD-TYPE   21   14
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  M0            2                 21
  MX            0                 14
D47V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          1    1
  19P LOSS WILD-TYPE   23   13
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  N0            1                 23
  N1            1                 13
D47V7, continuous
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                 34 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A2LY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZL         TCGA-DR-A0ZM         TCGA-DS-A0VK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VL         TCGA-DS-A0VM         TCGA-DS-A3LQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A43B 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A1H6         TCGA-EX-A3L1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-HG-A2PA         TCGA-HM-A3JJ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"19P LOSS WILD-TYPE" 
D47V8, continuous

Clustering(48) Variable = 20p loss
D48V1, survival
                    sevent
clus2                 0  1
  20P LOSS CNV        2  0
  20P LOSS WILD-TYPE 32  7
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 39 
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 0                  7 
$`20P LOSS CNV`
TCGA-EA-A1QT TCGA-EX-A1H6 
        0.26         7.92 

$`20P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZL 
       53.13        35.61         2.43        40.93        78.31        70.85 
TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       42.38        36.76         2.66        69.93        95.08         6.02 
TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B 
        1.74         1.32         0.82         0.62         0.66         1.78 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-FU-A3TQ TCGA-FU-A3WB TCGA-FU-A3YQ 
        0.07         1.02         1.45         1.58         0.79         3.48 
TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
       25.41        21.67         5.52 

      20P LOSS CNV 20P LOSS WILD-TYPE 
              0.26               0.07 
      20P LOSS CNV 20P LOSS WILD-TYPE 
              7.92             177.04 
      20P LOSS CNV 20P LOSS WILD-TYPE 
              4.09               5.52 
[1] "0.3 - 7.9 (4.1)"   "0.1 - 177.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
      "20P LOSS CNV" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"       "20P LOSS CNV" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 39 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EA-A439         TCGA-EA-A43B 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3TQ         TCGA-FU-A3WB         TCGA-FU-A3YQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JJ         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D48V2, continuous
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          0    3
  20P LOSS WILD-TYPE   13   26
     clus
vv    20P LOSS CNV 20P LOSS WILD-TYPE
  NO             0                 13
  YES            3                 26
D48V4, continuous
D48V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          1    1
  20P LOSS WILD-TYPE   22   13
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  M0            1                 22
  MX            1                 13
D48V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS CNV          2    0
  20P LOSS WILD-TYPE   22   14
    clus
vv   20P LOSS CNV 20P LOSS WILD-TYPE
  N0            2                 22
  N1            0                 14
D48V7, continuous
[1] "Remove cluster labels:" "20P LOSS CNV"          
clus
      20P LOSS CNV 20P LOSS WILD-TYPE 
                 2                 34 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A1M5         TCGA-C5-A1MF         TCGA-C5-A1MI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-C5-A2LY         TCGA-DR-A0ZL         TCGA-DR-A0ZM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VK         TCGA-DS-A0VL         TCGA-DS-A0VM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VN         TCGA-DS-A3LQ         TCGA-EA-A3HQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HR         TCGA-EA-A3HS         TCGA-EA-A3HT 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY         TCGA-FU-A3HZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3NI         TCGA-FU-A3TQ         TCGA-FU-A3WB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3YQ         TCGA-HG-A2PA         TCGA-HM-A3JJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" 
D48V8, continuous

Clustering(49) Variable = 21q loss
D49V1, survival
                    sevent
clus2                 0  1
  21Q LOSS CNV        6  0
  21Q LOSS WILD-TYPE 28  7
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 6                 35 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 0                  7 
$`21Q LOSS CNV`
TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-FU-A23L TCGA-FU-A3NI 
       30.41        70.85         2.66         1.32         1.22         1.45 

$`21Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        36.56       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-C5-A2LY TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        40.93        78.31        42.38        36.76 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS 
       69.93        95.08         6.02         0.26         1.74         0.82 
TCGA-EA-A3HT TCGA-EA-A439 TCGA-EA-A43B TCGA-EX-A1H5 TCGA-EX-A1H6 TCGA-EX-A3L1 
        0.62         0.66         1.78         5.85         7.92         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3TQ 
        1.22         0.99         2.17         0.07         1.02         1.58 
TCGA-FU-A3WB TCGA-FU-A3YQ TCGA-HG-A2PA TCGA-HM-A3JJ TCGA-HM-A3JK 
        0.79         3.48        25.41        21.67         5.52 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              1.22               0.07 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             70.85             177.04 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             2.055              5.850 
[1] "1.2 - 70.8 (2.1)"  "0.1 - 177.0 (5.8)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-C5-A1BI 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1BK         TCGA-C5-A1BN         TCGA-C5-A1M5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MF         TCGA-C5-A1MI         TCGA-C5-A1MK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-C5-A1MN         TCGA-C5-A2LY         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EA-A439 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A43B         TCGA-EX-A1H5         TCGA-EX-A1H6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A3L1         TCGA-FU-A23K         TCGA-FU-A23L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-FU-A2QG         TCGA-FU-A3EO         TCGA-FU-A3HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HZ         TCGA-FU-A3NI         TCGA-FU-A3TQ 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3WB         TCGA-FU-A3YQ         TCGA-HG-A2PA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-HM-A3JJ         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr="     "2.2e+08"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          0    6
  21Q LOSS WILD-TYPE   13   23
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  NO             0                 13
  YES            6                 23
D49V4, continuous
D49V5, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          4    2
  21Q LOSS WILD-TYPE   19   12
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  M0            4                 19
  MX            2                 12
D49V6, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          5    1
  21Q LOSS WILD-TYPE   19   13
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  N0            5                 19
  N1            1                 13
D49V7, continuous
D49V8, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
                    "DISTANT.METASTASIS" 
                                      V6 
                 "LYMPH.NODE.METASTASIS" 
                                      V7 
                 "NUMBER.OF.LYMPH.NODES" 
                                      V8 
                       "TUMOR.STAGECODE" 
> q(save="no")
