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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/287498/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/SKCM/2173730/1.GDAC_clinicalDataPicker.Finished/SKCM.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-TM", "-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=SKCM-TM"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=138, in cluster file=236, common to both=126
[1] "Reduce the number of clustering variables from 80 to 72."
[1]  72 126
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               19               107 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               19               107 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               43                83 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               43                83 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               114 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               114 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               116 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               116 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14               112 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               14               112 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               108 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               18               108 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               114 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               12               114 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               116 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               116 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               14               112 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               14               112 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3               123 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3               123 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               43                83 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               43                83 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               120 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               120 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               58                68 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               58                68 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56                70 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               56                70 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               100 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               26               100 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               39                87 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               39                87 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                119 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                119 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                122 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                122 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                116 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                116 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                121 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                121 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                105 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                105 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                115 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                115 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                110 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                110 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 9                117 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 9                117 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                118 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 8                118 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                116 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                116 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                110 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                110 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                111 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                15                111 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                118 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                118 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                119 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                119 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                116 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                10                116 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                38                 88 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                38                 88 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                46                 80 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                46                 80 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                111 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                111 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                 92 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                34                 92 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               123 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               123 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10               116 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10               116 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5               121 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5               121 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               115 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               115 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               115 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               115 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               116 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               116 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               116 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               116 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10               116 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10               116 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11               115 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11               115 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               109 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               109 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28                98 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28                98 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               114 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               12               114 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               53                73 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               53                73 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14               112 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14               112 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               73                53 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               73                53 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               56                70 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               56                70 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                55                 71 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                55                 71 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                61                 65 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                61                 65 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                 94 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                 94 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                35                 91 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                35                 91 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                118 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                118 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                113 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                113 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                107 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                107 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                33                 93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                33                 93 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                116 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                116 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                116 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                116 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                23                103 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                23                103 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 97 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                113 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                113 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                102 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                24                102 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                23                103 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                23                103 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                116 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                10                116 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                114 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                12                114 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                121 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                121 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                109 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                17                109 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                118 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                118 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               123 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3               123 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [8] "RADIATIONTHERAPY"                      
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "BATCHNUMBER"                           

Input Data has 10 rows and 126 columns.

[1] "Batch" "10"   
[1] "Last Follow UP"
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1HW 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MT TCGA-EE-A2MU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N 
          NA           NA           NA           NA           NA         1340 
TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
          NA         2433         2443           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZC 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZK TCGA-FS-A1ZM 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
          NA           NA           NA            6         3664           NA 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        2577           NA           NA           NA           NA         1204 
Variable 1:'AGE':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 126 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=15, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2               0 1
  1P GAIN MUTATED   1 3
  1P GAIN WILD-TYPE 6 5
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                11 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                 5 
$`1P GAIN MUTATED`
TCGA-ER-A19F TCGA-ER-A3ET TCGA-GN-A266 TCGA-GN-A26A 
       26.37        80.32        10.09        32.48 

$`1P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 TCGA-GN-A262 
       12.59       131.08        44.05        79.99         0.20       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
      117.93        84.72        64.41        62.76        39.58 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            10.09              0.20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            80.32            131.08 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           29.425            64.410 
[1] "10.1 - 80.3 (29.4)" "0.2 - 131.1 (64.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
[1] "hr=" "4.1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   11
  1P GAIN WILD-TYPE   38   69
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               8                38
  MALE                11                69

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2               0 1
  1Q GAIN MUTATED   2 5
  1Q GAIN WILD-TYPE 5 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                7                 8 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                 3 
$`1Q GAIN MUTATED`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A3ET TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       12.59        26.37        80.32        10.09        64.41        32.48 
TCGA-GN-A26D 
       39.58 

$`1Q GAIN WILD-TYPE`
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
      131.08        44.05        79.99         0.20       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A268 
       84.72        62.76 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            10.09              0.20 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            80.32            131.08 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           32.480            82.355 
[1] "10.1 - 80.3 (32.5)" "0.2 - 131.1 (82.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "8.8"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15   28
  1Q GAIN WILD-TYPE   31   52
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              15                31
  MALE                28                52

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2               0 1
  2P GAIN MUTATED   1 0
  2P GAIN WILD-TYPE 6 8
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                14 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 8 
$`2P GAIN MUTATED`
TCGA-ER-A19N 
       44.05 

$`2P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37       131.08        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            44.05              0.20 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            44.05            131.08 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           44.050            63.585 
[1] "44.0 - 44.0 (44.0)" "0.2 - 131.1 (63.6)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A1A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V2, continuous
[1] "Remove cluster labels:" "2P GAIN MUTATED"       
clus
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19O 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   10
  2P GAIN WILD-TYPE   44   70
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               2                44
  MALE                10                70

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2               0 1
  2Q GAIN MUTATED   1 0
  2Q GAIN WILD-TYPE 6 8
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                14 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 8 
$`2Q GAIN MUTATED`
TCGA-ER-A19N 
       44.05 

$`2Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37       131.08        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            44.05              0.20 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            44.05            131.08 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           44.050            63.585 
[1] "44.0 - 44.0 (44.0)" "0.2 - 131.1 (63.6)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A1A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
D4V2, continuous
[1] "Remove cluster labels:" "2Q GAIN MUTATED"       
clus
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19O 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    8
  2Q GAIN WILD-TYPE   44   72
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               2                44
  MALE                 8                72

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2               0 1
  3P GAIN MUTATED   1 1
  3P GAIN WILD-TYPE 6 7
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 7 
$`3P GAIN MUTATED`
TCGA-ER-A3ET TCGA-GN-A266 
       80.32        10.09 

$`3P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 
       12.59        26.37       131.08        44.05        79.99         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.41        62.76        32.48 
TCGA-GN-A26D 
       39.58 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            10.09              0.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            80.32            131.08 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           45.205            62.760 
[1] "10.1 - 80.3 (45.2)" "0.2 - 131.1 (62.8)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                13 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"3P GAIN WILD-TYPE" 
D5V2, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-FW-A3I3        TCGA-GN-A262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    8
  3P GAIN WILD-TYPE   40   72
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6                40
  MALE                 8                72

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2               0 1
  3Q GAIN MUTATED   1 2
  3Q GAIN WILD-TYPE 6 6
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                12 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 6 
$`3Q GAIN MUTATED`
TCGA-ER-A3ET TCGA-GN-A266 TCGA-GN-A26A 
       80.32        10.09        32.48 

$`3Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 
       12.59        26.37       131.08        44.05        79.99         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
      120.46       117.93        84.72        64.41        62.76        39.58 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            10.09              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            80.32            131.08 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           32.480            63.585 
[1] "10.1 - 80.3 (32.5)" "0.2 - 131.1 (63.6)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
[1] "hr=" "2.6"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8   10
  3Q GAIN WILD-TYPE   38   70
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8                38
  MALE                10                70

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2               0 1
  4P GAIN MUTATED   2 1
  4P GAIN WILD-TYPE 5 7
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                12 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 7 
$`4P GAIN MUTATED`
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26D 
       80.32       117.93        39.58 

$`4P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 
       12.59        26.37       131.08        44.05        79.99         0.20 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46        84.72        10.09        64.41        62.76        32.48 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            39.58              0.20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           117.93            131.08 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           80.320            53.405 
[1] "39.6 - 117.9 (80.3)" "0.2 - 131.1 (53.4)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr=" "2.1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    8
  4P GAIN WILD-TYPE   42   72
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4                42
  MALE                 8                72

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2               0 1
  4Q GAIN MUTATED   1 1
  4Q GAIN WILD-TYPE 6 7
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                13 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                 7 
$`4Q GAIN MUTATED`
TCGA-GN-A264 TCGA-GN-A26D 
      117.93        39.58 

$`4Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46        84.72        10.09        64.41        62.76 
TCGA-GN-A26A 
       32.48 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            39.58              0.20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           117.93            131.08 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           78.755            62.760 
[1] "39.6 - 117.9 (78.8)" "0.2 - 131.1 (62.8)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                13 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26A 
"4Q GAIN WILD-TYPE" 
D8V2, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    7
  4Q GAIN WILD-TYPE   43   73
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               3                43
  MALE                 7                73

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2               0 1
  5P GAIN MUTATED   1 0
  5P GAIN WILD-TYPE 6 8
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                14 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 8 
$`5P GAIN MUTATED`
TCGA-FW-A3I3 
         0.2 

$`5P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20             10.09 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20            131.08 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            0.200            63.585 
[1] "0.2 - 0.2 (0.2)"     "10.1 - 131.1 (63.6)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A262        TCGA-GN-A264 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D9V2, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A262        TCGA-GN-A264 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    7
  5P GAIN WILD-TYPE   39   73
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                39
  MALE                 7                73

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2               0 1
  5Q GAIN WILD-TYPE 7 8
5Q GAIN WILD-TYPE 
               15 
[1] 8
$`5Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

5Q GAIN WILD-TYPE 
              0.2 
5Q GAIN WILD-TYPE 
           131.08 
5Q GAIN WILD-TYPE 
            62.76 
[1] "0.2 - 131.1 (62.8)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    3
  5Q GAIN WILD-TYPE   46   77
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               0                46
  MALE                 3                77

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2               0 1
  6P GAIN MUTATED   3 3
  6P GAIN WILD-TYPE 4 5
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                6                 9 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                 5 
$`6P GAIN MUTATED`
TCGA-ER-A19N TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       44.05         0.20       117.93        10.09        32.48        39.58 

$`6P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 
       12.59        26.37       131.08        79.99        80.32       120.46 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       84.72        64.41        62.76 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20             12.59 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           117.93            131.08 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            36.03             79.99 
[1] "0.2 - 117.9 (36.0)"  "12.6 - 131.1 (80.0)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
[1] "hr=" "2"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     19   24
  6P GAIN WILD-TYPE   27   56
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              19                27
  MALE                24                56

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2               0 1
  6Q GAIN WILD-TYPE 7 8
6Q GAIN WILD-TYPE 
               15 
[1] 8
$`6Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

6Q GAIN WILD-TYPE 
              0.2 
6Q GAIN WILD-TYPE 
           131.08 
6Q GAIN WILD-TYPE 
            62.76 
[1] "0.2 - 131.1 (62.8)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    3
  6Q GAIN WILD-TYPE   43   77
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               3                43
  MALE                 3                77

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2               0 1
  7P GAIN MUTATED   2 4
  7P GAIN WILD-TYPE 5 4
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                 9 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                 4 
$`7P GAIN MUTATED`
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20       117.93        10.09        64.41        32.48        39.58 

$`7P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A268 
      120.46        84.72        62.76 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20             12.59 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           117.93            131.08 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            36.03             79.99 
[1] "0.2 - 117.9 (36.0)"  "12.6 - 131.1 (80.0)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "2.9"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     22   36
  7P GAIN WILD-TYPE   24   44
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              22                24
  MALE                36                44

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2               0 1
  7Q GAIN MUTATED   2 3
  7Q GAIN WILD-TYPE 5 5
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 5 
$`7Q GAIN MUTATED`
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20       117.93        64.41        32.48        39.58 

$`7Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
      120.46        84.72        10.09        62.76 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20             10.09 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           117.93            131.08 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           39.580            71.375 
[1] "0.2 - 117.9 (39.6)"  "10.1 - 131.1 (71.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.7"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     22   34
  7Q GAIN WILD-TYPE   24   46
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              22                24
  MALE                34                46

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2               0 1
  8P GAIN MUTATED   3 3
  8P GAIN WILD-TYPE 4 5
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                 9 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                 5 
$`8P GAIN MUTATED`
TCGA-ER-A19L TCGA-ER-A19N TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
      131.08        44.05         0.20        64.41        32.48        39.58 

$`8P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A264 
       12.59        26.37        79.99        80.32       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       84.72        10.09        62.76 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.20             10.09 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           131.08            120.46 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           41.815            79.990 
[1] "0.2 - 131.1 (41.8)"  "10.1 - 120.5 (80.0)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
[1] "hr=" "1.4"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      7   19
  8P GAIN WILD-TYPE   39   61
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               7                39
  MALE                19                61

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   4 3
  8Q GAIN WILD-TYPE 3 5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                 8 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                 5 
$`8Q GAIN MUTATED`
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A3ET TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26A 
      131.08        44.05        80.32         0.20        64.41        32.48 
TCGA-GN-A26D 
       39.58 

$`8Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       12.59        26.37        79.99       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        62.76 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.20             10.09 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           131.08            120.46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           44.050            71.375 
[1] "0.2 - 131.1 (44.0)"  "10.1 - 120.5 (71.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
[1] "hr=" "2"  
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12   27
  8Q GAIN WILD-TYPE   34   53
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              12                34
  MALE                27                53

Clustering(17) Variable = 11p gain mutation analysis
D17V1, survival
                    sevent
clus2                0 1
  11P GAIN MUTATED   1 0
  11P GAIN WILD-TYPE 6 8
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 14 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  8 
$`11P GAIN MUTATED`
TCGA-ER-A19N 
       44.05 

$`11P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37       131.08        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             44.05               0.20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             44.05             131.08 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            44.050             63.585 
[1] "44.0 - 44.0 (44.0)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D17V2, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    6
  11P GAIN WILD-TYPE   45   74
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                1                 45
  MALE                  6                 74

Clustering(18) Variable = 11q gain mutation analysis
D18V1, survival
                    sevent
clus2                0 1
  11Q GAIN MUTATED   1 0
  11Q GAIN WILD-TYPE 6 8
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 14 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  8 
$`11Q GAIN MUTATED`
TCGA-ER-A19N 
       44.05 

$`11Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37       131.08        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             44.05               0.20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             44.05             131.08 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            44.050             63.585 
[1] "44.0 - 44.0 (44.0)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D18V2, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    4
  11Q GAIN WILD-TYPE   46   76
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                0                 46
  MALE                  4                 76

Clustering(19) Variable = 12p gain mutation analysis
D19V1, survival
                    sevent
clus2                0 1
  12P GAIN MUTATED   0 2
  12P GAIN WILD-TYPE 7 6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                  6 
$`12P GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A26A 
      131.08        32.48 

$`12P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26D 
       39.58 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             32.48               0.20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            131.08             120.46 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             81.78              62.76 
[1] "32.5 - 131.1 (81.8)" "0.2 - 120.5 (62.8)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"12P GAIN WILD-TYPE" 
D19V2, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    8
  12P GAIN WILD-TYPE   44   72
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 44
  MALE                  8                 72

Clustering(20) Variable = 12q gain mutation analysis
D20V1, survival
                    sevent
clus2                0 1
  12Q GAIN MUTATED   0 2
  12Q GAIN WILD-TYPE 7 6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  6 
$`12Q GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A26A 
      131.08        32.48 

$`12Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26D 
       39.58 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             32.48               0.20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            131.08             120.46 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             81.78              62.76 
[1] "32.5 - 131.1 (81.8)" "0.2 - 120.5 (62.8)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" 
D20V2, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    4
  12Q GAIN WILD-TYPE   45   76
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 45
  MALE                  4                 76

Clustering(21) Variable = 13q gain mutation analysis
D21V1, survival
                    sevent
clus2                0 1
  13Q GAIN MUTATED   1 3
  13Q GAIN WILD-TYPE 6 5
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                 11 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                  5 
$`13Q GAIN MUTATED`
TCGA-ER-A19L TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
      131.08        44.05        64.41        62.76 

$`13Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 TCGA-GN-A262 
       12.59        26.37        79.99        80.32         0.20       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
      117.93        84.72        10.09        32.48        39.58 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             44.05               0.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            131.08             120.46 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            63.585             39.580 
[1] "44.0 - 131.1 (63.6)" "0.2 - 120.5 (39.6)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7   14
  13Q GAIN WILD-TYPE   39   66
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 39
  MALE                 14                 66

Clustering(22) Variable = 14q gain mutation analysis
D22V1, survival
                    sevent
clus2                0 1
  14Q GAIN MUTATED   1 1
  14Q GAIN WILD-TYPE 6 7
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  7 
$`14Q GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A26D 
      131.08        39.58 

$`14Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A 
       32.48 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             39.58               0.20 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            131.08             120.46 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             85.33              62.76 
[1] "39.6 - 131.1 (85.3)" "0.2 - 120.5 (62.8)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" 
D22V2, continuous
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    7
  14Q GAIN WILD-TYPE   42   73
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 42
  MALE                  7                 73

Clustering(23) Variable = 15q gain mutation analysis
D23V1, survival
                    sevent
clus2                0 1
  15Q GAIN MUTATED   0 1
  15Q GAIN WILD-TYPE 7 7
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 14 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                  7 
$`15Q GAIN MUTATED`
TCGA-GN-A264 
      117.93 

$`15Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            117.93               0.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            117.93             131.08 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
           117.930             53.405 
[1] "117.9 - 117.9 (117.9)" "0.2 - 131.1 (53.4)"   
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D23V2, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6   10
  15Q GAIN WILD-TYPE   40   70
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                6                 40
  MALE                 10                 70

Clustering(24) Variable = 16p gain mutation analysis
D24V1, survival
                    sevent
clus2                0 1
  16P GAIN MUTATED   0 1
  16P GAIN WILD-TYPE 7 7
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 14 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  7 
$`16P GAIN MUTATED`
TCGA-ER-A19D 
       12.59 

$`16P GAIN WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       26.37       131.08        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.59               0.20 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.59             131.08 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            12.590             63.585 
[1] "12.6 - 12.6 (12.6)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D24V2, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    5
  16P GAIN WILD-TYPE   42   75
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 42
  MALE                  5                 75

Clustering(25) Variable = 16q gain mutation analysis
D25V1, survival
                    sevent
clus2                0 1
  16Q GAIN MUTATED   0 1
  16Q GAIN WILD-TYPE 7 7
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 14 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  7 
$`16Q GAIN MUTATED`
TCGA-ER-A19D 
       12.59 

$`16Q GAIN WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       26.37       131.08        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             12.59               0.20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             12.59             131.08 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            12.590             63.585 
[1] "12.6 - 12.6 (12.6)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D25V2, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    5
  16Q GAIN WILD-TYPE   43   75
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 43
  MALE                  5                 75

Clustering(26) Variable = 17p gain mutation analysis
D26V1, survival
                    sevent
clus2                0 1
  17P GAIN MUTATED   1 0
  17P GAIN WILD-TYPE 6 8
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 14 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                  8 
$`17P GAIN MUTATED`
TCGA-GN-A26D 
       39.58 

$`17P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A 
       62.76        32.48 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             39.58               0.20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             39.58             131.08 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            39.580             63.585 
[1] "39.6 - 39.6 (39.6)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D26V2, continuous
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    6
  17P GAIN WILD-TYPE   42   74
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 42
  MALE                  6                 74

Clustering(27) Variable = 17q gain mutation analysis
D27V1, survival
                    sevent
clus2                0 1
  17Q GAIN MUTATED   1 1
  17Q GAIN WILD-TYPE 6 7
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  7 
$`17Q GAIN MUTATED`
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

$`17Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A26A 
       32.48 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             39.58               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             62.76             131.08 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             51.17              64.41 
[1] "39.6 - 62.8 (51.2)" "0.2 - 131.1 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26A 
"17Q GAIN WILD-TYPE" 
D27V2, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A26A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    9
  17Q GAIN WILD-TYPE   39   71
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                7                 39
  MALE                  9                 71

Clustering(28) Variable = 18p gain mutation analysis
D28V1, survival
                    sevent
clus2                0 1
  18P GAIN MUTATED   1 2
  18P GAIN WILD-TYPE 6 6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 12 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  6 
$`18P GAIN MUTATED`
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       64.41        32.48        39.58 

$`18P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        0.20       120.46       117.93        84.72        10.09        62.76 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             32.48               0.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             64.41             131.08 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            39.580             71.375 
[1] "32.5 - 64.4 (39.6)" "0.2 - 131.1 (71.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
[1] "hr=" "2"  
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    9
  18P GAIN WILD-TYPE   40   71
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                6                 40
  MALE                  9                 71

Clustering(29) Variable = 18q gain mutation analysis
D29V1, survival
                    sevent
clus2                0 1
  18Q GAIN MUTATED   1 2
  18Q GAIN WILD-TYPE 6 6
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 12 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  6 
$`18Q GAIN MUTATED`
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       64.41        32.48        39.58 

$`18Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        0.20       120.46       117.93        84.72        10.09        62.76 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.48               0.20 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             64.41             131.08 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            39.580             71.375 
[1] "32.5 - 64.4 (39.6)" "0.2 - 131.1 (71.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
[1] "hr=" "2"  
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    5
  18Q GAIN WILD-TYPE   43   75
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 43
  MALE                  5                 75

Clustering(30) Variable = 19p gain mutation analysis
D30V1, survival
                    sevent
clus2                0 1
  19P GAIN WILD-TYPE 7 8
19P GAIN WILD-TYPE 
                15 
[1] 8
$`19P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

19P GAIN WILD-TYPE 
               0.2 
19P GAIN WILD-TYPE 
            131.08 
19P GAIN WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    4
  19P GAIN WILD-TYPE   43   76
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                 43
  MALE                  4                 76

Clustering(31) Variable = 19q gain mutation analysis
D31V1, survival
                    sevent
clus2                0 1
  19Q GAIN MUTATED   1 0
  19Q GAIN WILD-TYPE 6 8
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 14 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  8 
$`19Q GAIN MUTATED`
TCGA-ER-A3ET 
       80.32 

$`19Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 
       12.59        26.37       131.08        44.05        79.99         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             80.32               0.20 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             80.32             131.08 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            80.320             53.405 
[1] "80.3 - 80.3 (80.3)" "0.2 - 131.1 (53.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-FW-A3I3 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D31V2, continuous
[1] "Remove cluster labels:" "19Q GAIN MUTATED"      
clus
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      6    4
  19Q GAIN WILD-TYPE   40   76
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                6                 40
  MALE                  4                 76

Clustering(32) Variable = 20p gain mutation analysis
D32V1, survival
                    sevent
clus2                0 1
  20P GAIN MUTATED   2 3
  20P GAIN WILD-TYPE 5 5
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  5 
$`20P GAIN MUTATED`
TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
      131.08         0.20       117.93        32.48        39.58 

$`20P GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 
       12.59        26.37        44.05        79.99        80.32       120.46 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       84.72        10.09        64.41        62.76 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20              10.09 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            131.08             120.46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            39.580             63.585 
[1] "0.2 - 131.1 (39.6)"  "10.1 - 120.5 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
[1] "hr=" "1.4"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   26
  20P GAIN WILD-TYPE   34   54
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               12                 34
  MALE                 26                 54

Clustering(33) Variable = 20q gain mutation analysis
D33V1, survival
                    sevent
clus2                0 1
  20Q GAIN MUTATED   2 3
  20Q GAIN WILD-TYPE 5 5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                  5 
$`20Q GAIN MUTATED`
TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
      131.08         0.20       117.93        32.48        39.58 

$`20Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 
       12.59        26.37        44.05        79.99        80.32       120.46 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       84.72        10.09        64.41        62.76 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20              10.09 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            131.08             120.46 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            39.580             63.585 
[1] "0.2 - 131.1 (39.6)"  "10.1 - 120.5 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
[1] "hr=" "1.4"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     15   31
  20Q GAIN WILD-TYPE   31   49
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               15                 31
  MALE                 31                 49

Clustering(34) Variable = 21q gain mutation analysis
D34V1, survival
                    sevent
clus2                0 1
  21Q GAIN MUTATED   2 2
  21Q GAIN WILD-TYPE 5 6
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 11 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                  6 
$`21Q GAIN MUTATED`
TCGA-ER-A19D TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A26D 
       12.59       131.08         0.20        39.58 

$`21Q GAIN WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A264 
       26.37        44.05        79.99        80.32       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       84.72        10.09        64.41        62.76        32.48 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20              10.09 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            131.08             120.46 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            26.085             64.410 
[1] "0.2 - 131.1 (26.1)"  "10.1 - 120.5 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
[1] "hr=" "1.5"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7    8
  21Q GAIN WILD-TYPE   39   72
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                7                 39
  MALE                  8                 72

Clustering(35) Variable = 22q gain mutation analysis
D35V1, survival
                    sevent
clus2                0 1
  22Q GAIN MUTATED   4 3
  22Q GAIN WILD-TYPE 3 5
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                  8 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                  5 
$`22Q GAIN MUTATED`
TCGA-ER-A3ET TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
       80.32         0.20       117.93        84.72        64.41        32.48 
TCGA-GN-A26D 
       39.58 

$`22Q GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-GN-A262 
       12.59        26.37       131.08        44.05        79.99       120.46 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        62.76 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20              10.09 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            117.93             131.08 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            64.410             53.405 
[1] "0.2 - 117.9 (64.4)"  "10.1 - 131.1 (53.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     15   19
  22Q GAIN WILD-TYPE   31   61
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               15                 31
  MALE                 19                 61

Clustering(36) Variable = Xq gain mutation analysis
D36V1, survival
                   sevent
clus2               0 1
  XQ GAIN MUTATED   0 1
  XQ GAIN WILD-TYPE 7 7
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                14 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 7 
$`XQ GAIN MUTATED`
TCGA-GN-A264 
      117.93 

$`XQ GAIN WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           117.93              0.20 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           117.93            131.08 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
          117.930            53.405 
[1] "117.9 - 117.9 (117.9)" "0.2 - 131.1 (53.4)"   
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D36V2, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    3
  XQ GAIN WILD-TYPE   46   77
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               0                46
  MALE                 3                77

Clustering(37) Variable = 1p loss mutation analysis
D37V1, survival
                   sevent
clus2               0 1
  1P LOSS MUTATED   1 1
  1P LOSS WILD-TYPE 6 7
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 7 
$`1P LOSS MUTATED`
TCGA-ER-A19L TCGA-GN-A26D 
      131.08        39.58 

$`1P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       12.59        26.37        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A 
       32.48 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            39.58              0.20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           131.08            120.46 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            85.33             62.76 
[1] "39.6 - 131.1 (85.3)" "0.2 - 120.5 (62.8)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                13 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19N        TCGA-ER-A1A1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A 
"1P LOSS WILD-TYPE" 
D37V2, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19N        TCGA-ER-A19O 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3    7
  1P LOSS WILD-TYPE   43   73
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               3                43
  MALE                 7                73

Clustering(38) Variable = 1q loss mutation analysis
D38V1, survival
                   sevent
clus2               0 1
  1Q LOSS WILD-TYPE 7 8
1Q LOSS WILD-TYPE 
               15 
[1] 8
$`1Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

1Q LOSS WILD-TYPE 
              0.2 
1Q LOSS WILD-TYPE 
           131.08 
1Q LOSS WILD-TYPE 
            62.76 
[1] "0.2 - 131.1 (62.8)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    3
  1Q LOSS WILD-TYPE   44   77
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                44
  MALE                 3                77

Clustering(39) Variable = 2p loss mutation analysis
D39V1, survival
                   sevent
clus2               0 1
  2P LOSS MUTATED   1 1
  2P LOSS WILD-TYPE 6 7
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                13 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                 7 
$`2P LOSS MUTATED`
TCGA-GN-A264 TCGA-GN-A26D 
      117.93        39.58 

$`2P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46        84.72        10.09        64.41        62.76 
TCGA-GN-A26A 
       32.48 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            39.58              0.20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           117.93            131.08 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           78.755            62.760 
[1] "39.6 - 117.9 (78.8)" "0.2 - 131.1 (62.8)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                13 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26A 
"2P LOSS WILD-TYPE" 
D39V2, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    7
  2P LOSS WILD-TYPE   42   73
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                42
  MALE                 7                73

Clustering(40) Variable = 2q loss mutation analysis
D40V1, survival
                   sevent
clus2               0 1
  2Q LOSS MUTATED   1 0
  2Q LOSS WILD-TYPE 6 8
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                14 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                 8 
$`2Q LOSS MUTATED`
TCGA-GN-A26D 
       39.58 

$`2Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A 
       62.76        32.48 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            39.58              0.20 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            39.58            131.08 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           39.580            63.585 
[1] "39.6 - 39.6 (39.6)" "0.2 - 131.1 (63.6)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D40V2, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    6
  2Q LOSS WILD-TYPE   41   74
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                41
  MALE                 6                74

Clustering(41) Variable = 3p loss mutation analysis
D41V1, survival
                   sevent
clus2               0 1
  3P LOSS MUTATED   1 0
  3P LOSS WILD-TYPE 6 8
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                14 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 8 
$`3P LOSS MUTATED`
TCGA-GN-A262 
      120.46 

$`3P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           120.46              0.20 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           120.46            131.08 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
          120.460            53.405 
[1] "120.5 - 120.5 (120.5)" "0.2 - 131.1 (53.4)"   
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A264 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D41V2, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    6
  3P LOSS WILD-TYPE   42   74
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                42
  MALE                 6                74

Clustering(42) Variable = 3q loss mutation analysis
D42V1, survival
                   sevent
clus2               0 1
  3Q LOSS MUTATED   1 2
  3Q LOSS WILD-TYPE 6 6
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                12 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                 6 
$`3Q LOSS MUTATED`
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
      120.46       117.93        62.76 

$`3Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20        84.72        10.09        64.41        32.48        39.58 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            62.76              0.20 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           120.46            131.08 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
          117.930            41.815 
[1] "62.8 - 120.5 (117.9)" "0.2 - 131.1 (41.8)"  
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    4
  3Q LOSS WILD-TYPE   40   76
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6                40
  MALE                 4                76

Clustering(43) Variable = 4p loss mutation analysis
D43V1, survival
                   sevent
clus2               0 1
  4P LOSS MUTATED   0 2
  4P LOSS WILD-TYPE 7 6
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                13 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 6 
$`4P LOSS MUTATED`
TCGA-ER-A19D TCGA-GN-A266 
       12.59        10.09 

$`4P LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       26.37       131.08        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.41        62.76        32.48 
TCGA-GN-A26D 
       39.58 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            10.09              0.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            12.59            131.08 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            11.34             64.41 
[1] "10.1 - 12.6 (11.3)" "0.2 - 131.1 (64.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                13 
       TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N        TCGA-ER-A1A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26D 
"4P LOSS WILD-TYPE" 
D43V2, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                14 
       TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N        TCGA-ER-A19O 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    4
  4P LOSS WILD-TYPE   40   76
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                40
  MALE                 4                76

Clustering(44) Variable = 4q loss mutation analysis
D44V1, survival
                   sevent
clus2               0 1
  4Q LOSS MUTATED   0 2
  4Q LOSS WILD-TYPE 7 6
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                13 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                 6 
$`4Q LOSS MUTATED`
TCGA-ER-A19D TCGA-GN-A266 
       12.59        10.09 

$`4Q LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       26.37       131.08        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.41        62.76        32.48 
TCGA-GN-A26D 
       39.58 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            10.09              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            12.59            131.08 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            11.34             64.41 
[1] "10.1 - 12.6 (11.3)" "0.2 - 131.1 (64.4)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                13 
       TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N        TCGA-ER-A1A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262        TCGA-GN-A264 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" 
D44V2, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                14 
       TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N        TCGA-ER-A19O 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      7    4
  4Q LOSS WILD-TYPE   39   76
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               7                39
  MALE                 4                76

Clustering(45) Variable = 5p loss mutation analysis
D45V1, survival
                   sevent
clus2               0 1
  5P LOSS MUTATED   1 2
  5P LOSS WILD-TYPE 6 6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                12 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                 6 
$`5P LOSS MUTATED`
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
      120.46        10.09        62.76 

$`5P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20       117.93        84.72        64.41        32.48        39.58 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            10.09              0.20 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           120.46            131.08 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            62.76             54.23 
[1] "10.1 - 120.5 (62.8)" "0.2 - 131.1 (54.2)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6   11
  5P LOSS WILD-TYPE   40   69
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               6                40
  MALE                11                69

Clustering(46) Variable = 5q loss mutation analysis
D46V1, survival
                   sevent
clus2               0 1
  5Q LOSS MUTATED   1 2
  5Q LOSS WILD-TYPE 6 6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                12 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 6 
$`5Q LOSS MUTATED`
TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
      120.46        10.09        62.76 

$`5Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20       117.93        84.72        64.41        32.48        39.58 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            10.09              0.20 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           120.46            131.08 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            62.76             54.23 
[1] "10.1 - 120.5 (62.8)" "0.2 - 131.1 (54.2)" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      9   19
  5Q LOSS WILD-TYPE   37   61
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               9                37
  MALE                19                61

Clustering(47) Variable = 6p loss mutation analysis
D47V1, survival
                   sevent
clus2               0 1
  6P LOSS WILD-TYPE 7 8
6P LOSS WILD-TYPE 
               15 
[1] 8
$`6P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

6P LOSS WILD-TYPE 
              0.2 
6P LOSS WILD-TYPE 
           131.08 
6P LOSS WILD-TYPE 
            62.76 
[1] "0.2 - 131.1 (62.8)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6    6
  6P LOSS WILD-TYPE   40   74
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               6                40
  MALE                 6                74

Clustering(48) Variable = 6q loss mutation analysis
D48V1, survival
                   sevent
clus2               0 1
  6Q LOSS MUTATED   1 5
  6Q LOSS WILD-TYPE 6 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                 9 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                 3 
$`6Q LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       12.59        26.37         0.20        64.41        62.76        32.48 

$`6Q LOSS WILD-TYPE`
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A264 
      131.08        44.05        79.99        80.32       120.46       117.93 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       84.72        10.09        39.58 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.20             10.09 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            64.41            131.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           29.425            80.320 
[1] "0.2 - 64.4 (29.4)"   "10.1 - 131.1 (80.3)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "14" 
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     22   31
  6Q LOSS WILD-TYPE   24   49
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              22                24
  MALE                31                49

Clustering(49) Variable = 8p loss mutation analysis
D49V1, survival
                   sevent
clus2               0 1
  8P LOSS MUTATED   0 1
  8P LOSS WILD-TYPE 7 7
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                14 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 7 
$`8P LOSS MUTATED`
TCGA-GN-A264 
      117.93 

$`8P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           117.93              0.20 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           117.93            131.08 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
          117.930            53.405 
[1] "117.9 - 117.9 (117.9)" "0.2 - 131.1 (53.4)"   
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D49V2, continuous
[1] "Remove cluster labels:" "8P LOSS MUTATED"       
clus
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3   11
  8P LOSS WILD-TYPE   43   69
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                43
  MALE                11                69

Clustering(50) Variable = 9p loss mutation analysis
D50V1, survival
                   sevent
clus2               0 1
  9P LOSS MUTATED   2 5
  9P LOSS WILD-TYPE 5 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                 8 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                 3 
$`9P LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A268 TCGA-GN-A26A 
       12.59        26.37       131.08         0.20        62.76        32.48 
TCGA-GN-A26D 
       39.58 

$`9P LOSS WILD-TYPE`
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
       44.05        79.99        80.32       120.46       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 
       10.09        64.41 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20             10.09 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           131.08            120.46 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           32.480            80.155 
[1] "0.2 - 131.1 (32.5)"  "10.1 - 120.5 (80.2)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
[1] "hr=" "2.7"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     30   43
  9P LOSS WILD-TYPE   16   37
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              30                16
  MALE                43                37

Clustering(51) Variable = 9q loss mutation analysis
D51V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   3 4
  9Q LOSS WILD-TYPE 4 4
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                7                 8 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                 4 
$`9Q LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A 
       12.59        26.37         0.20       120.46        62.76        32.48 
TCGA-GN-A26D 
       39.58 

$`9Q LOSS WILD-TYPE`
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A265 
      131.08        44.05        79.99        80.32       117.93        84.72 
TCGA-GN-A266 TCGA-GN-A267 
       10.09        64.41 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.20             10.09 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           120.46            131.08 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           32.480            80.155 
[1] "0.2 - 120.5 (32.5)"  "10.1 - 131.1 (80.2)"
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
[1] "hr=" "2.7"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27   29
  9Q LOSS WILD-TYPE   19   51
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              27                19
  MALE                29                51

Clustering(52) Variable = 10p loss mutation analysis
D52V1, survival
                    sevent
clus2                0 1
  10P LOSS MUTATED   1 7
  10P LOSS WILD-TYPE 6 1
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                  7 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                  1 
$`10P LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       12.59       131.08        80.32       117.93        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A 
       62.76        32.48 

$`10P LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 
       26.37        44.05        79.99         0.20       120.46        84.72 
TCGA-GN-A26D 
       39.58 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             10.09               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            131.08             120.46 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            63.585             44.050 
[1] "10.1 - 131.1 (63.6)" "0.2 - 120.5 (44.0)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
[1] "hr=" "4.5"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25   30
  10P LOSS WILD-TYPE   21   50
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               25                 21
  MALE                 30                 50

Clustering(53) Variable = 10q loss mutation analysis
D53V1, survival
                    sevent
clus2                0 1
  10Q LOSS MUTATED   1 6
  10Q LOSS WILD-TYPE 6 2
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 7                  8 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                  2 
$`10Q LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19L TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 
       12.59       131.08       120.46       117.93        10.09        64.41 
TCGA-GN-A26A 
       32.48 

$`10Q LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 TCGA-GN-A265 
       26.37        44.05        79.99        80.32         0.20        84.72 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             10.09               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            131.08              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            64.410             53.405 
[1] "10.1 - 131.1 (64.4)" "0.2 - 84.7 (53.4)"  
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     26   35
  10Q LOSS WILD-TYPE   20   45
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               26                 20
  MALE                 35                 45

Clustering(54) Variable = 11p loss mutation analysis
D54V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   2 5
  11P LOSS WILD-TYPE 5 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                  8 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  3 
$`11P LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 
       12.59       131.08         0.20       120.46       117.93        64.41 
TCGA-GN-A26A 
       32.48 

$`11P LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A265 TCGA-GN-A266 
       26.37        44.05        79.99        80.32        84.72        10.09 
TCGA-GN-A268 TCGA-GN-A26D 
       62.76        39.58 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20              10.09 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            131.08              84.72 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            64.410             53.405 
[1] "0.2 - 131.1 (64.4)" "10.1 - 84.7 (53.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18   14
  11P LOSS WILD-TYPE   28   66
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               18                 28
  MALE                 14                 66

Clustering(55) Variable = 11q loss mutation analysis
D55V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   2 5
  11Q LOSS WILD-TYPE 5 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                  8 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  3 
$`11Q LOSS MUTATED`
TCGA-ER-A19D TCGA-ER-A19L TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
       12.59       131.08         0.20       117.93        64.41        32.48 
TCGA-GN-A26D 
       39.58 

$`11Q LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 TCGA-GN-A265 
       26.37        44.05        79.99        80.32       120.46        84.72 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        62.76 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20              10.09 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            131.08             120.46 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            39.580             71.375 
[1] "0.2 - 131.1 (39.6)"  "10.1 - 120.5 (71.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
[1] "hr=" "1.6"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     17   18
  11Q LOSS WILD-TYPE   29   62
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               17                 29
  MALE                 18                 62

Clustering(56) Variable = 12p loss mutation analysis
D56V1, survival
                    sevent
clus2                0 1
  12P LOSS WILD-TYPE 7 8
12P LOSS WILD-TYPE 
                15 
[1] 8
$`12P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

12P LOSS WILD-TYPE 
               0.2 
12P LOSS WILD-TYPE 
            131.08 
12P LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    4
  12P LOSS WILD-TYPE   42   76
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                4                 42
  MALE                  4                 76

Clustering(57) Variable = 12q loss mutation analysis
D57V1, survival
                    sevent
clus2                0 1
  12Q LOSS WILD-TYPE 7 8
12Q LOSS WILD-TYPE 
                15 
[1] 8
$`12Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

12Q LOSS WILD-TYPE 
               0.2 
12Q LOSS WILD-TYPE 
            131.08 
12Q LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      6    7
  12Q LOSS WILD-TYPE   40   73
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                6                 40
  MALE                  7                 73

Clustering(58) Variable = 13q loss mutation analysis
D58V1, survival
                    sevent
clus2                0 1
  13Q LOSS MUTATED   1 1
  13Q LOSS WILD-TYPE 6 7
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  7 
$`13Q LOSS MUTATED`
TCGA-GN-A266 TCGA-GN-A26D 
       10.09        39.58 

$`13Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46       117.93        84.72        64.41        62.76 
TCGA-GN-A26A 
       32.48 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.09               0.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             39.58             131.08 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            24.835             64.410 
[1] "10.1 - 39.6 (24.8)" "0.2 - 131.1 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A267         TCGA-GN-A268 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" 
D58V2, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9   10
  13Q LOSS WILD-TYPE   37   70
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                 37
  MALE                 10                 70

Clustering(59) Variable = 14q loss mutation analysis
D59V1, survival
                    sevent
clus2                0 1
  14Q LOSS MUTATED   0 4
  14Q LOSS WILD-TYPE 7 4
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 11 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                  4 
$`14Q LOSS MUTATED`
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        64.41        62.76        32.48 

$`14Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
        0.20       120.46        84.72        10.09        39.58 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             32.48               0.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            117.93             131.08 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            63.585             44.050 
[1] "32.5 - 117.9 (63.6)" "0.2 - 131.1 (44.0)" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   23
  14Q LOSS WILD-TYPE   36   57
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                 36
  MALE                 23                 57

Clustering(60) Variable = 15q loss mutation analysis
D60V1, survival
                    sevent
clus2                0 1
  15Q LOSS MUTATED   0 1
  15Q LOSS WILD-TYPE 7 7
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 14 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  7 
$`15Q LOSS MUTATED`
TCGA-GN-A266 
       10.09 

$`15Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46       117.93        84.72        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             10.09               0.20 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             10.09             131.08 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            10.090             63.585 
[1] "10.1 - 10.1 (10.1)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A267         TCGA-GN-A268 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D60V2, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    6
  15Q LOSS WILD-TYPE   42   74
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 42
  MALE                  6                 74

Clustering(61) Variable = 16p loss mutation analysis
D61V1, survival
                    sevent
clus2                0 1
  16P LOSS MUTATED   1 2
  16P LOSS WILD-TYPE 6 6
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 12 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                  6 
$`16P LOSS MUTATED`
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
      120.46       117.93        62.76 

$`16P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20        84.72        10.09        64.41        32.48        39.58 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             62.76               0.20 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            120.46             131.08 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
           117.930             41.815 
[1] "62.8 - 120.5 (117.9)" "0.2 - 131.1 (41.8)"  
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    5
  16P LOSS WILD-TYPE   41   75
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                5                 41
  MALE                  5                 75

Clustering(62) Variable = 16q loss mutation analysis
D62V1, survival
                    sevent
clus2                0 1
  16Q LOSS MUTATED   2 3
  16Q LOSS WILD-TYPE 5 5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 10 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                  5 
$`16Q LOSS MUTATED`
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        0.20       120.46       117.93        64.41        62.76 

$`16Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        32.48        39.58 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20              10.09 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            120.46             131.08 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            64.410             41.815 
[1] "0.2 - 120.5 (64.4)"  "10.1 - 131.1 (41.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   14
  16Q LOSS WILD-TYPE   37   66
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                9                 37
  MALE                 14                 66

Clustering(63) Variable = 17p loss mutation analysis
D63V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   1 1
  17P LOSS WILD-TYPE 6 7
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  7 
$`17P LOSS MUTATED`
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$`17P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      120.46       117.93        84.72        64.41        62.76        32.48 
TCGA-GN-A26D 
       39.58 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20              12.59 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.09             131.08 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             5.145             64.410 
[1] "0.2 - 10.1 (5.1)"    "12.6 - 131.1 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17P LOSS WILD-TYPE" 
D63V2, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A262         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A267         TCGA-GN-A268 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     11   18
  17P LOSS WILD-TYPE   35   62
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               11                 35
  MALE                 18                 62

Clustering(64) Variable = 17q loss mutation analysis
D64V1, survival
                    sevent
clus2                0 1
  17Q LOSS MUTATED   1 1
  17Q LOSS WILD-TYPE 6 7
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  7 
$`17Q LOSS MUTATED`
TCGA-ER-A19L TCGA-FW-A3I3 
      131.08         0.20 

$`17Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A262 
       12.59        26.37        44.05        79.99        80.32       120.46 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
      117.93        84.72        10.09        64.41        62.76        32.48 
TCGA-GN-A26D 
       39.58 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20              10.09 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            131.08             120.46 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             65.64              62.76 
[1] "0.2 - 131.1 (65.6)"  "10.1 - 120.5 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-GN-A262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" 
D64V2, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5    8
  17Q LOSS WILD-TYPE   41   72
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                5                 41
  MALE                  8                 72

Clustering(65) Variable = 18p loss mutation analysis
D65V1, survival
                    sevent
clus2                0 1
  18P LOSS WILD-TYPE 7 8
18P LOSS WILD-TYPE 
                15 
[1] 8
$`18P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

18P LOSS WILD-TYPE 
               0.2 
18P LOSS WILD-TYPE 
            131.08 
18P LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   15
  18P LOSS WILD-TYPE   37   65
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                9                 37
  MALE                 15                 65

Clustering(66) Variable = 18q loss mutation analysis
D66V1, survival
                    sevent
clus2                0 1
  18Q LOSS WILD-TYPE 7 8
18Q LOSS WILD-TYPE 
                15 
[1] 8
$`18Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

18Q LOSS WILD-TYPE 
               0.2 
18Q LOSS WILD-TYPE 
            131.08 
18Q LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      9   14
  18Q LOSS WILD-TYPE   37   66
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                9                 37
  MALE                 14                 66

Clustering(67) Variable = 19p loss mutation analysis
D67V1, survival
                    sevent
clus2                0 1
  19P LOSS WILD-TYPE 7 8
19P LOSS WILD-TYPE 
                15 
[1] 8
$`19P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

19P LOSS WILD-TYPE 
               0.2 
19P LOSS WILD-TYPE 
            131.08 
19P LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8    2
  19P LOSS WILD-TYPE   38   78
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                8                 38
  MALE                  2                 78

Clustering(68) Variable = 19q loss mutation analysis
D68V1, survival
                    sevent
clus2                0 1
  19Q LOSS MUTATED   1 1
  19Q LOSS WILD-TYPE 6 7
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  7 
$`19Q LOSS MUTATED`
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

$`19Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 
       62.76 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             32.48               0.20 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             39.58             131.08 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             36.03              64.41 
[1] "32.5 - 39.6 (36.0)" "0.2 - 131.1 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19Q LOSS WILD-TYPE" 
D68V2, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    4
  19Q LOSS WILD-TYPE   38   76
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                 38
  MALE                  4                 76

Clustering(69) Variable = 20p loss mutation analysis
D69V1, survival
                    sevent
clus2                0 1
  20P LOSS WILD-TYPE 7 8
20P LOSS WILD-TYPE 
                15 
[1] 8
$`20P LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.20       120.46       117.93        84.72        10.09        64.41 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       62.76        32.48        39.58 

20P LOSS WILD-TYPE 
               0.2 
20P LOSS WILD-TYPE 
            131.08 
20P LOSS WILD-TYPE 
             62.76 
[1] "0.2 - 131.1 (62.8)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE   45   76
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                1                 45
  MALE                  4                 76

Clustering(70) Variable = 21q loss mutation analysis
D70V1, survival
                    sevent
clus2                0 1
  21Q LOSS MUTATED   0 2
  21Q LOSS WILD-TYPE 7 6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  6 
$`21Q LOSS MUTATED`
TCGA-GN-A266 TCGA-GN-A268 
       10.09        62.76 

$`21Q LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        0.20       120.46       117.93        84.72        64.41        32.48 
TCGA-GN-A26D 
       39.58 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             10.09               0.20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             62.76             131.08 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            36.425             64.410 
[1] "10.1 - 62.8 (36.4)" "0.2 - 131.1 (64.4)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 13 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A267         TCGA-GN-A26A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" 
D70V2, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 14 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A19O         TCGA-ER-A1A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FW-A3I3         TCGA-GN-A262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7   10
  21Q LOSS WILD-TYPE   39   70
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                7                 39
  MALE                 10                 70

Clustering(71) Variable = 22q loss mutation analysis
D71V1, survival
                    sevent
clus2                0 1
  22Q LOSS MUTATED   0 1
  22Q LOSS WILD-TYPE 7 7
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 14 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  7 
$`22Q LOSS MUTATED`
TCGA-ER-A19D 
       12.59 

$`22Q LOSS WILD-TYPE`
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FW-A3I3 
       26.37       131.08        44.05        79.99        80.32         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
      120.46       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             12.59               0.20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             12.59             131.08 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            12.590             63.585 
[1] "12.6 - 12.6 (12.6)" "0.2 - 131.1 (63.6)"
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19L 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 14 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FW-A3I3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D71V2, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 15 
        TCGA-ER-A19F         TCGA-ER-A19L         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19O         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3I3         TCGA-GN-A262         TCGA-GN-A264 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A265         TCGA-GN-A266         TCGA-GN-A267 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268         TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3    5
  22Q LOSS WILD-TYPE   43   75
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                3                 43
  MALE                  5                 75

Clustering(72) Variable = Xq loss mutation analysis
D72V1, survival
                   sevent
clus2               0 1
  XQ LOSS MUTATED   1 0
  XQ LOSS WILD-TYPE 6 8
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                14 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                0                 8 
$`XQ LOSS MUTATED`
TCGA-GN-A262 
      120.46 

$`XQ LOSS WILD-TYPE`
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       12.59        26.37       131.08        44.05        79.99        80.32 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
        0.20       117.93        84.72        10.09        64.41        62.76 
TCGA-GN-A26A TCGA-GN-A26D 
       32.48        39.58 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           120.46              0.20 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           120.46            131.08 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
          120.460            53.405 
[1] "120.5 - 120.5 (120.5)" "0.2 - 131.1 (53.4)"   
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                14 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3        TCGA-GN-A264 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D72V2, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                15 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19L        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FW-A3I3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D72V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    1
  XQ LOSS WILD-TYPE   44   79
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               2                44
  MALE                 1                79
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
