
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_Cnvs_onlysig.41.3771/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.41.3771/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/145919/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC/1551578/1.GDAC_clinicalDataPicker.Finished/CESC.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"      "-oT=CESC"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=31, in cluster file=68, common to both=14
[1] "Reduce the number of clustering variables from 35 to 18."
[1] 18 14
[1] "Amp Peak  1(3q26.31) mutation analysis"
[1] 3
  AMP PEAK  1(3Q26.31) MUTATED AMP PEAK  1(3Q26.31) WILD-TYPE 
                            11                              3 
  AMP PEAK  1(3Q26.31) MUTATED AMP PEAK  1(3Q26.31) WILD-TYPE 
                            11                              3 
[1] "Amp Peak  5(8q24.21) mutation analysis"
[1] 3
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                             7                              7 
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                             7                              7 
[1] "Amp Peak  6(8q24.21) mutation analysis"
[1] 3
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                             7                              7 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                             7                              7 
[1] "Amp Peak  7(9p24.1) mutation analysis"
[1] 3
  AMP PEAK  7(9P24.1) MUTATED AMP PEAK  7(9P24.1) WILD-TYPE 
                            3                            11 
  AMP PEAK  7(9P24.1) MUTATED AMP PEAK  7(9P24.1) WILD-TYPE 
                            3                            11 
[1] "Amp Peak 10(11q22.1) mutation analysis"
[1] 3
  AMP PEAK 10(11Q22.1) MUTATED AMP PEAK 10(11Q22.1) WILD-TYPE 
                             3                             11 
  AMP PEAK 10(11Q22.1) MUTATED AMP PEAK 10(11Q22.1) WILD-TYPE 
                             3                             11 
[1] "Amp Peak 15(20q11.21) mutation analysis"
[1] 3
  AMP PEAK 15(20Q11.21) MUTATED AMP PEAK 15(20Q11.21) WILD-TYPE 
                              6                               8 
  AMP PEAK 15(20Q11.21) MUTATED AMP PEAK 15(20Q11.21) WILD-TYPE 
                              6                               8 
[1] "Del Peak  3(2q37.2) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.2) MUTATED DEL PEAK  3(2Q37.2) WILD-TYPE 
                            7                             7 
  DEL PEAK  3(2Q37.2) MUTATED DEL PEAK  3(2Q37.2) WILD-TYPE 
                            7                             7 
[1] "Del Peak  4(3p22.1) mutation analysis"
[1] 3
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                            7                             7 
  DEL PEAK  4(3P22.1) MUTATED DEL PEAK  4(3P22.1) WILD-TYPE 
                            7                             7 
[1] "Del Peak  5(3p14.1) mutation analysis"
[1] 3
  DEL PEAK  5(3P14.1) MUTATED DEL PEAK  5(3P14.1) WILD-TYPE 
                            8                             6 
  DEL PEAK  5(3P14.1) MUTATED DEL PEAK  5(3P14.1) WILD-TYPE 
                            8                             6 
[1] "Del Peak  6(4q35.2) mutation analysis"
[1] 3
  DEL PEAK  6(4Q35.2) MUTATED DEL PEAK  6(4Q35.2) WILD-TYPE 
                            4                            10 
  DEL PEAK  6(4Q35.2) MUTATED DEL PEAK  6(4Q35.2) WILD-TYPE 
                            4                            10 
[1] "Del Peak  7(5q35.3) mutation analysis"
[1] 3
  DEL PEAK  7(5Q35.3) MUTATED DEL PEAK  7(5Q35.3) WILD-TYPE 
                            8                             6 
  DEL PEAK  7(5Q35.3) MUTATED DEL PEAK  7(5Q35.3) WILD-TYPE 
                            8                             6 
[1] "Del Peak 10(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 10(10Q23.31) MUTATED DEL PEAK 10(10Q23.31) WILD-TYPE 
                              3                              11 
  DEL PEAK 10(10Q23.31) MUTATED DEL PEAK 10(10Q23.31) WILD-TYPE 
                              3                              11 
[1] "Del Peak 11(11q14.2) mutation analysis"
[1] 3
  DEL PEAK 11(11Q14.2) MUTATED DEL PEAK 11(11Q14.2) WILD-TYPE 
                             3                             11 
  DEL PEAK 11(11Q14.2) MUTATED DEL PEAK 11(11Q14.2) WILD-TYPE 
                             3                             11 
[1] "Del Peak 12(11q25) mutation analysis"
[1] 3
  DEL PEAK 12(11Q25) MUTATED DEL PEAK 12(11Q25) WILD-TYPE 
                           7                            7 
  DEL PEAK 12(11Q25) MUTATED DEL PEAK 12(11Q25) WILD-TYPE 
                           7                            7 
[1] "Del Peak 13(13q12.12) mutation analysis"
[1] 3
  DEL PEAK 13(13Q12.12) MUTATED DEL PEAK 13(13Q12.12) WILD-TYPE 
                              8                               6 
  DEL PEAK 13(13Q12.12) MUTATED DEL PEAK 13(13Q12.12) WILD-TYPE 
                              8                               6 
[1] "Del Peak 14(13q13.2) mutation analysis"
[1] 3
  DEL PEAK 14(13Q13.2) MUTATED DEL PEAK 14(13Q13.2) WILD-TYPE 
                             8                              6 
  DEL PEAK 14(13Q13.2) MUTATED DEL PEAK 14(13Q13.2) WILD-TYPE 
                             8                              6 
[1] "Del Peak 18(19p13.3) mutation analysis"
[1] 3
  DEL PEAK 18(19P13.3) MUTATED DEL PEAK 18(19P13.3) WILD-TYPE 
                             4                             10 
  DEL PEAK 18(19P13.3) MUTATED DEL PEAK 18(19P13.3) WILD-TYPE 
                             4                             10 
[1] "Del Peak 19(21q21.1) mutation analysis"
[1] 3
  DEL PEAK 19(21Q21.1) MUTATED DEL PEAK 19(21Q21.1) WILD-TYPE 
                             4                             10 
  DEL PEAK 19(21Q21.1) MUTATED DEL PEAK 19(21Q21.1) WILD-TYPE 
                             4                             10 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 14 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1505          925         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K 
        2127         2892            8           NA          178           37 
TCGA-FU-A23L TCGA-FU-A2QG 
          37           30 
Variable 1:'AGE':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 14 columns, 1 survival variables, and 1 non-survival variables.
AGE, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = Amp Peak  1(3q26.31) mutation analysis
D1V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  1(3Q26.31) MUTATED"   "AMP PEAK  1(3Q26.31) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  1(3Q26.31) MUTATED" "AMP PEAK  1(3Q26.31) WILD-TYPE" 
[1] "hr=" "1"  
D1V2, continuous

Clustering(2) Variable = Amp Peak  5(8q24.21) mutation analysis
D2V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  5(8Q24.21) WILD-TYPE"   "AMP PEAK  5(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  5(8Q24.21) MUTATED" "AMP PEAK  5(8Q24.21) WILD-TYPE" 
[1] "hr="     "1.1e+09"
D2V2, continuous

Clustering(3) Variable = Amp Peak  6(8q24.21) mutation analysis
D3V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"AMP PEAK  6(8Q24.21) WILD-TYPE" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  6(8Q24.21) MUTATED"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"AMP PEAK  6(8Q24.21) WILD-TYPE" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  6(8Q24.21) MUTATED"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"AMP PEAK  6(8Q24.21) WILD-TYPE" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK  6(8Q24.21) MUTATED"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK  6(8Q24.21) WILD-TYPE"   "AMP PEAK  6(8Q24.21) MUTATED" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "AMP PEAK  6(8Q24.21) MUTATED" "AMP PEAK  6(8Q24.21) WILD-TYPE" 
[1] "hr="     "2.6e+09"
D3V2, continuous

Clustering(4) Variable = Amp Peak  7(9p24.1) mutation analysis
D4V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"AMP PEAK  7(9P24.1) WILD-TYPE"   "AMP PEAK  7(9P24.1) MUTATED" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"AMP PEAK  7(9P24.1) WILD-TYPE"   "AMP PEAK  7(9P24.1) MUTATED" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "AMP PEAK  7(9P24.1) MUTATED" "AMP PEAK  7(9P24.1) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"AMP PEAK  7(9P24.1) WILD-TYPE"   "AMP PEAK  7(9P24.1) MUTATED" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"AMP PEAK  7(9P24.1) WILD-TYPE" "AMP PEAK  7(9P24.1) WILD-TYPE" 
[1] "hr="   "7e+08"
D4V2, continuous

Clustering(5) Variable = Amp Peak 10(11q22.1) mutation analysis
D5V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK 10(11Q22.1) MUTATED" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK 10(11Q22.1) MUTATED"   "AMP PEAK 10(11Q22.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK 10(11Q22.1) MUTATED" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK 10(11Q22.1) MUTATED"   "AMP PEAK 10(11Q22.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "AMP PEAK 10(11Q22.1) MUTATED" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
  "AMP PEAK 10(11Q22.1) MUTATED"   "AMP PEAK 10(11Q22.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"AMP PEAK 10(11Q22.1) WILD-TYPE" "AMP PEAK 10(11Q22.1) WILD-TYPE" 
[1] "hr="     "2.6e+09"
D5V2, continuous

Clustering(6) Variable = Amp Peak 15(20q11.21) mutation analysis
D6V1, survival
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "AMP PEAK 15(20Q11.21) MUTATED" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
"AMP PEAK 15(20Q11.21) WILD-TYPE"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "AMP PEAK 15(20Q11.21) MUTATED" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
"AMP PEAK 15(20Q11.21) WILD-TYPE"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "AMP PEAK 15(20Q11.21) MUTATED" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "AMP PEAK 15(20Q11.21) MUTATED"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
"AMP PEAK 15(20Q11.21) WILD-TYPE"   "AMP PEAK 15(20Q11.21) MUTATED" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"AMP PEAK 15(20Q11.21) WILD-TYPE" "AMP PEAK 15(20Q11.21) WILD-TYPE" 
[1] "hr="     "2.6e+09"
D6V2, continuous

Clustering(7) Variable = Del Peak  3(2q37.2) mutation analysis
D7V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  3(2Q37.2) MUTATED"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"DEL PEAK  3(2Q37.2) WILD-TYPE" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  3(2Q37.2) MUTATED"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"DEL PEAK  3(2Q37.2) WILD-TYPE" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  3(2Q37.2) MUTATED" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  3(2Q37.2) MUTATED"   "DEL PEAK  3(2Q37.2) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
"DEL PEAK  3(2Q37.2) WILD-TYPE" "DEL PEAK  3(2Q37.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  3(2Q37.2) WILD-TYPE"   "DEL PEAK  3(2Q37.2) MUTATED" 
[1] "hr="     "2.6e+09"
D7V2, continuous

Clustering(8) Variable = Del Peak  4(3p22.1) mutation analysis
D8V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  4(3P22.1) MUTATED"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  4(3P22.1) WILD-TYPE"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  4(3P22.1) MUTATED"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  4(3P22.1) WILD-TYPE"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  4(3P22.1) WILD-TYPE" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  4(3P22.1) MUTATED"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  4(3P22.1) WILD-TYPE"   "DEL PEAK  4(3P22.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  4(3P22.1) MUTATED" "DEL PEAK  4(3P22.1) WILD-TYPE" 
[1] "hr=" "1"  
D8V2, continuous

Clustering(9) Variable = Del Peak  5(3p14.1) mutation analysis
D9V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  5(3P14.1) WILD-TYPE" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  5(3P14.1) WILD-TYPE" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  5(3P14.1) WILD-TYPE" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  5(3P14.1) MUTATED"   "DEL PEAK  5(3P14.1) MUTATED" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  5(3P14.1) MUTATED" "DEL PEAK  5(3P14.1) WILD-TYPE" 
[1] "hr=" "1"  
D9V2, continuous

Clustering(10) Variable = Del Peak  6(4q35.2) mutation analysis
D10V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
"DEL PEAK  6(4Q35.2) WILD-TYPE" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  6(4Q35.2) MUTATED" "DEL PEAK  6(4Q35.2) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
"DEL PEAK  6(4Q35.2) WILD-TYPE"   "DEL PEAK  6(4Q35.2) MUTATED" 
[1] "hr="   "7e+08"
D10V2, continuous

Clustering(11) Variable = Del Peak  7(5q35.3) mutation analysis
D11V1, survival
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  7(5Q35.3) WILD-TYPE" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  7(5Q35.3) WILD-TYPE" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
                   TCGA-BI-A0VR                    TCGA-BI-A0VS 
"DEL PEAK  7(5Q35.3) WILD-TYPE" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DR-A0ZL                    TCGA-DR-A0ZM 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-DS-A0VK                    TCGA-DS-A0VL 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
                   TCGA-DS-A0VM                    TCGA-DS-A0VN 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EA-A1QT                    TCGA-EK-A2PI 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-EX-A1H5                    TCGA-FU-A23K 
  "DEL PEAK  7(5Q35.3) MUTATED" "DEL PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-FU-A23L                    TCGA-FU-A2QG 
  "DEL PEAK  7(5Q35.3) MUTATED"   "DEL PEAK  7(5Q35.3) MUTATED" 
[1] "hr="     "1.1e+09"
D11V2, continuous

Clustering(12) Variable = Del Peak 10(10q23.31) mutation analysis
D12V1, survival
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"DEL PEAK 10(10Q23.31) WILD-TYPE"   "DEL PEAK 10(10Q23.31) MUTATED" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"DEL PEAK 10(10Q23.31) WILD-TYPE"   "DEL PEAK 10(10Q23.31) MUTATED" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
"DEL PEAK 10(10Q23.31) WILD-TYPE" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 10(10Q23.31) MUTATED" "DEL PEAK 10(10Q23.31) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
"DEL PEAK 10(10Q23.31) WILD-TYPE"   "DEL PEAK 10(10Q23.31) MUTATED" 
[1] "hr="     "2.8e+10"
D12V2, continuous

Clustering(13) Variable = Del Peak 11(11q14.2) mutation analysis
D13V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 11(11Q14.2) MUTATED"   "DEL PEAK 11(11Q14.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 11(11Q14.2) MUTATED" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 11(11Q14.2) MUTATED"   "DEL PEAK 11(11Q14.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 11(11Q14.2) MUTATED" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 11(11Q14.2) MUTATED"   "DEL PEAK 11(11Q14.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 11(11Q14.2) MUTATED" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
"DEL PEAK 11(11Q14.2) WILD-TYPE" "DEL PEAK 11(11Q14.2) WILD-TYPE" 
[1] "hr="   "7e+08"
D13V2, continuous

Clustering(14) Variable = Del Peak 12(11q25) mutation analysis
D14V1, survival
                  TCGA-BI-A0VR                   TCGA-BI-A0VS 
"DEL PEAK 12(11Q25) WILD-TYPE"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DR-A0ZL                   TCGA-DR-A0ZM 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-DS-A0VK                   TCGA-DS-A0VL 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DS-A0VM                   TCGA-DS-A0VN 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-EA-A1QT                   TCGA-EK-A2PI 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-EX-A1H5                   TCGA-FU-A23K 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-FU-A23L                   TCGA-FU-A2QG 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-BI-A0VR                   TCGA-BI-A0VS 
"DEL PEAK 12(11Q25) WILD-TYPE"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DR-A0ZL                   TCGA-DR-A0ZM 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-DS-A0VK                   TCGA-DS-A0VL 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DS-A0VM                   TCGA-DS-A0VN 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-EA-A1QT                   TCGA-EK-A2PI 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-EX-A1H5                   TCGA-FU-A23K 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-FU-A23L                   TCGA-FU-A2QG 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-BI-A0VR                   TCGA-BI-A0VS 
"DEL PEAK 12(11Q25) WILD-TYPE"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DR-A0ZL                   TCGA-DR-A0ZM 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-DS-A0VK                   TCGA-DS-A0VL 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-DS-A0VM                   TCGA-DS-A0VN 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-EA-A1QT                   TCGA-EK-A2PI 
  "DEL PEAK 12(11Q25) MUTATED"   "DEL PEAK 12(11Q25) MUTATED" 
                  TCGA-EX-A1H5                   TCGA-FU-A23K 
  "DEL PEAK 12(11Q25) MUTATED" "DEL PEAK 12(11Q25) WILD-TYPE" 
                  TCGA-FU-A23L                   TCGA-FU-A2QG 
"DEL PEAK 12(11Q25) WILD-TYPE" "DEL PEAK 12(11Q25) WILD-TYPE" 
[1] "hr="     "1.1e+09"
D14V2, continuous

Clustering(15) Variable = Del Peak 13(13q12.12) mutation analysis
D15V1, survival
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 13(13Q12.12) WILD-TYPE"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
"DEL PEAK 13(13Q12.12) WILD-TYPE" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 13(13Q12.12) WILD-TYPE"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
"DEL PEAK 13(13Q12.12) WILD-TYPE" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-BI-A0VR                      TCGA-BI-A0VS 
"DEL PEAK 13(13Q12.12) WILD-TYPE"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-DR-A0ZL                      TCGA-DR-A0ZM 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VK                      TCGA-DS-A0VL 
"DEL PEAK 13(13Q12.12) WILD-TYPE" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-DS-A0VM                      TCGA-DS-A0VN 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EA-A1QT                      TCGA-EK-A2PI 
  "DEL PEAK 13(13Q12.12) MUTATED"   "DEL PEAK 13(13Q12.12) MUTATED" 
                     TCGA-EX-A1H5                      TCGA-FU-A23K 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
                     TCGA-FU-A23L                      TCGA-FU-A2QG 
  "DEL PEAK 13(13Q12.12) MUTATED" "DEL PEAK 13(13Q12.12) WILD-TYPE" 
[1] "hr="     "2.8e+10"
D15V2, continuous

Clustering(16) Variable = Del Peak 14(13q13.2) mutation analysis
D16V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 14(13Q13.2) WILD-TYPE"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 14(13Q13.2) WILD-TYPE" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 14(13Q13.2) WILD-TYPE"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 14(13Q13.2) WILD-TYPE" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 14(13Q13.2) WILD-TYPE"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 14(13Q13.2) WILD-TYPE" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 14(13Q13.2) MUTATED"   "DEL PEAK 14(13Q13.2) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 14(13Q13.2) MUTATED" "DEL PEAK 14(13Q13.2) WILD-TYPE" 
[1] "hr="     "2.8e+10"
D16V2, continuous

Clustering(17) Variable = Del Peak 18(19p13.3) mutation analysis
D17V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 18(19P13.3) MUTATED"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"DEL PEAK 18(19P13.3) WILD-TYPE"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 18(19P13.3) MUTATED" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 18(19P13.3) MUTATED"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"DEL PEAK 18(19P13.3) WILD-TYPE"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 18(19P13.3) MUTATED" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
  "DEL PEAK 18(19P13.3) MUTATED"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
"DEL PEAK 18(19P13.3) WILD-TYPE"   "DEL PEAK 18(19P13.3) MUTATED" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 18(19P13.3) WILD-TYPE" "DEL PEAK 18(19P13.3) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 18(19P13.3) MUTATED" "DEL PEAK 18(19P13.3) WILD-TYPE" 
[1] "hr="     "2.6e+09"
D17V2, continuous

Clustering(18) Variable = Del Peak 19(21q21.1) mutation analysis
D18V1, survival
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 19(21Q21.1) WILD-TYPE"   "DEL PEAK 19(21Q21.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 19(21Q21.1) WILD-TYPE"   "DEL PEAK 19(21Q21.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-BI-A0VR                     TCGA-BI-A0VS 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DR-A0ZL                     TCGA-DR-A0ZM 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-DS-A0VK                     TCGA-DS-A0VL 
"DEL PEAK 19(21Q21.1) WILD-TYPE"   "DEL PEAK 19(21Q21.1) MUTATED" 
                    TCGA-DS-A0VM                     TCGA-DS-A0VN 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EA-A1QT                     TCGA-EK-A2PI 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-EX-A1H5                     TCGA-FU-A23K 
"DEL PEAK 19(21Q21.1) WILD-TYPE" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
                    TCGA-FU-A23L                     TCGA-FU-A2QG 
  "DEL PEAK 19(21Q21.1) MUTATED" "DEL PEAK 19(21Q21.1) WILD-TYPE" 
[1] "hr="   "7e+08"
D18V2, continuous
           V1.D              V2 
"Time to Death"           "AGE" 
> q(save="no")
