
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/282826/all_lesions.conf_99.cnv.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", "-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"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=138, in cluster file=275, common to both=138
[1]  51 138
[1] "Amp Peak  1(1p36.11) mutation analysis"
[1] 3
  AMP PEAK  1(1P36.11) MUTATED AMP PEAK  1(1P36.11) WILD-TYPE 
                            27                            111 
  AMP PEAK  1(1P36.11) MUTATED AMP PEAK  1(1P36.11) WILD-TYPE 
                            27                            111 
[1] "Amp Peak  2(1p12) mutation analysis"
[1] 3
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                         40                          98 
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                         40                          98 
[1] "Amp Peak  3(1q44) mutation analysis"
[1] 3
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         73                          65 
  AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE 
                         73                          65 
[1] "Amp Peak  4(3p13) mutation analysis"
[1] 3
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         31                         107 
  AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE 
                         31                         107 
[1] "Amp Peak  5(4q12) mutation analysis"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         24                         114 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         24                         114 
[1] "Amp Peak  6(5p15.33) mutation analysis"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            40                             98 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                            40                             98 
[1] "Amp Peak  7(5q35.3) mutation analysis"
[1] 3
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           16                           122 
  AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE 
                           16                           122 
[1] "Amp Peak  8(6p25.1) mutation analysis"
[1] 3
  AMP PEAK  8(6P25.1) MUTATED AMP PEAK  8(6P25.1) WILD-TYPE 
                           80                            58 
  AMP PEAK  8(6P25.1) MUTATED AMP PEAK  8(6P25.1) WILD-TYPE 
                           80                            58 
[1] "Amp Peak  9(6q12) mutation analysis"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         29                         109 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         29                         109 
[1] "Amp Peak 10(7p22.3) mutation analysis"
[1] 3
  AMP PEAK 10(7P22.3) MUTATED AMP PEAK 10(7P22.3) WILD-TYPE 
                           81                            57 
  AMP PEAK 10(7P22.3) MUTATED AMP PEAK 10(7P22.3) WILD-TYPE 
                           81                            57 
[1] "Amp Peak 11(7q34) mutation analysis"
[1] 3
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         85                          53 
  AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE 
                         85                          53 
[1] "Amp Peak 12(8q11.22) mutation analysis"
[1] 3
  AMP PEAK 12(8Q11.22) MUTATED AMP PEAK 12(8Q11.22) WILD-TYPE 
                            60                             78 
  AMP PEAK 12(8Q11.22) MUTATED AMP PEAK 12(8Q11.22) WILD-TYPE 
                            60                             78 
[1] "Amp Peak 13(8q24.3) mutation analysis"
[1] 3
  AMP PEAK 13(8Q24.3) MUTATED AMP PEAK 13(8Q24.3) WILD-TYPE 
                           70                            68 
  AMP PEAK 13(8Q24.3) MUTATED AMP PEAK 13(8Q24.3) WILD-TYPE 
                           70                            68 
[1] "Amp Peak 14(9p24.1) mutation analysis"
[1] 3
  AMP PEAK 14(9P24.1) MUTATED AMP PEAK 14(9P24.1) WILD-TYPE 
                           11                           127 
  AMP PEAK 14(9P24.1) MUTATED AMP PEAK 14(9P24.1) WILD-TYPE 
                           11                           127 
[1] "Amp Peak 15(11q13.3) mutation analysis"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            17                            121 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            17                            121 
[1] "Amp Peak 16(11q13.4) mutation analysis"
[1] 3
  AMP PEAK 16(11Q13.4) MUTATED AMP PEAK 16(11Q13.4) WILD-TYPE 
                            16                            122 
  AMP PEAK 16(11Q13.4) MUTATED AMP PEAK 16(11Q13.4) WILD-TYPE 
                            16                            122 
[1] "Amp Peak 17(12q15) mutation analysis"
[1] 3
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          17                          121 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          17                          121 
[1] "Amp Peak 18(13q31.3) mutation analysis"
[1] 3
  AMP PEAK 18(13Q31.3) MUTATED AMP PEAK 18(13Q31.3) WILD-TYPE 
                            36                            102 
  AMP PEAK 18(13Q31.3) MUTATED AMP PEAK 18(13Q31.3) WILD-TYPE 
                            36                            102 
[1] "Amp Peak 19(15q26.2) mutation analysis"
[1] 3
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            45                             93 
  AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE 
                            45                             93 
[1] "Amp Peak 20(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            54                             84 
  AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE 
                            54                             84 
[1] "Amp Peak 21(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            25                            113 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            25                            113 
[1] "Amp Peak 22(20q13.2) mutation analysis"
[1] 3
  AMP PEAK 22(20Q13.2) MUTATED AMP PEAK 22(20Q13.2) WILD-TYPE 
                            72                             66 
  AMP PEAK 22(20Q13.2) MUTATED AMP PEAK 22(20Q13.2) WILD-TYPE 
                            72                             66 
[1] "Amp Peak 23(22q13.2) mutation analysis"
[1] 3
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                            63                             75 
  AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE 
                            63                             75 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            34                            104 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            34                            104 
[1] "Del Peak  2(1p22.1) mutation analysis"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           32                           106 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           32                           106 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           36                           102 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           36                           102 
[1] "Del Peak  4(3q22.1) mutation analysis"
[1] 3
  DEL PEAK  4(3Q22.1) MUTATED DEL PEAK  4(3Q22.1) WILD-TYPE 
                           19                           119 
  DEL PEAK  4(3Q22.1) MUTATED DEL PEAK  4(3Q22.1) WILD-TYPE 
                           19                           119 
[1] "Del Peak  5(4p16.3) mutation analysis"
[1] 3
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           28                           110 
  DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE 
                           28                           110 
[1] "Del Peak  6(4q34.3) mutation analysis"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           36                           102 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           36                           102 
[1] "Del Peak  7(5q11.2) mutation analysis"
[1] 3
  DEL PEAK  7(5Q11.2) MUTATED DEL PEAK  7(5Q11.2) WILD-TYPE 
                           41                            97 
  DEL PEAK  7(5Q11.2) MUTATED DEL PEAK  7(5Q11.2) WILD-TYPE 
                           41                            97 
[1] "Del Peak  8(5q31.3) mutation analysis"
[1] 3
  DEL PEAK  8(5Q31.3) MUTATED DEL PEAK  8(5Q31.3) WILD-TYPE 
                           56                            82 
  DEL PEAK  8(5Q31.3) MUTATED DEL PEAK  8(5Q31.3) WILD-TYPE 
                           56                            82 
[1] "Del Peak  9(6q16.3) mutation analysis"
[1] 3
  DEL PEAK  9(6Q16.3) MUTATED DEL PEAK  9(6Q16.3) WILD-TYPE 
                           81                            57 
  DEL PEAK  9(6Q16.3) MUTATED DEL PEAK  9(6Q16.3) WILD-TYPE 
                           81                            57 
[1] "Del Peak 10(6q26) mutation analysis"
[1] 3
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         82                          56 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                         82                          56 
[1] "Del Peak 11(6q27) mutation analysis"
[1] 3
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         82                          56 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         82                          56 
[1] "Del Peak 12(9p23) mutation analysis"
[1] 3
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         92                          46 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         92                          46 
[1] "Del Peak 13(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          107                            31 
  DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE 
                          107                            31 
[1] "Del Peak 14(10p15.3) mutation analysis"
[1] 3
  DEL PEAK 14(10P15.3) MUTATED DEL PEAK 14(10P15.3) WILD-TYPE 
                            73                             65 
  DEL PEAK 14(10P15.3) MUTATED DEL PEAK 14(10P15.3) WILD-TYPE 
                            73                             65 
[1] "Del Peak 15(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             84                              54 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             84                              54 
[1] "Del Peak 16(10q26.3) mutation analysis"
[1] 3
  DEL PEAK 16(10Q26.3) MUTATED DEL PEAK 16(10Q26.3) WILD-TYPE 
                            84                             54 
  DEL PEAK 16(10Q26.3) MUTATED DEL PEAK 16(10Q26.3) WILD-TYPE 
                            84                             54 
[1] "Del Peak 17(11q23.3) mutation analysis"
[1] 3
  DEL PEAK 17(11Q23.3) MUTATED DEL PEAK 17(11Q23.3) WILD-TYPE 
                            76                             62 
  DEL PEAK 17(11Q23.3) MUTATED DEL PEAK 17(11Q23.3) WILD-TYPE 
                            76                             62 
[1] "Del Peak 18(12q24.33) mutation analysis"
[1] 3
  DEL PEAK 18(12Q24.33) MUTATED DEL PEAK 18(12Q24.33) WILD-TYPE 
                             31                             107 
  DEL PEAK 18(12Q24.33) MUTATED DEL PEAK 18(12Q24.33) WILD-TYPE 
                             31                             107 
[1] "Del Peak 19(13q34) mutation analysis"
[1] 3
  DEL PEAK 19(13Q34) MUTATED DEL PEAK 19(13Q34) WILD-TYPE 
                          33                          105 
  DEL PEAK 19(13Q34) MUTATED DEL PEAK 19(13Q34) WILD-TYPE 
                          33                          105 
[1] "Del Peak 20(14q32.2) mutation analysis"
[1] 3
  DEL PEAK 20(14Q32.2) MUTATED DEL PEAK 20(14Q32.2) WILD-TYPE 
                            42                             96 
  DEL PEAK 20(14Q32.2) MUTATED DEL PEAK 20(14Q32.2) WILD-TYPE 
                            42                             96 
[1] "Del Peak 21(15q13.3) mutation analysis"
[1] 3
  DEL PEAK 21(15Q13.3) MUTATED DEL PEAK 21(15Q13.3) WILD-TYPE 
                            35                            103 
  DEL PEAK 21(15Q13.3) MUTATED DEL PEAK 21(15Q13.3) WILD-TYPE 
                            35                            103 
[1] "Del Peak 22(15q15.3) mutation analysis"
[1] 3
  DEL PEAK 22(15Q15.3) MUTATED DEL PEAK 22(15Q15.3) WILD-TYPE 
                            32                            106 
  DEL PEAK 22(15Q15.3) MUTATED DEL PEAK 22(15Q15.3) WILD-TYPE 
                            32                            106 
[1] "Del Peak 23(16p13.3) mutation analysis"
[1] 3
  DEL PEAK 23(16P13.3) MUTATED DEL PEAK 23(16P13.3) WILD-TYPE 
                            23                            115 
  DEL PEAK 23(16P13.3) MUTATED DEL PEAK 23(16P13.3) WILD-TYPE 
                            23                            115 
[1] "Del Peak 24(16q12.1) mutation analysis"
[1] 3
  DEL PEAK 24(16Q12.1) MUTATED DEL PEAK 24(16Q12.1) WILD-TYPE 
                            45                             93 
  DEL PEAK 24(16Q12.1) MUTATED DEL PEAK 24(16Q12.1) WILD-TYPE 
                            45                             93 
[1] "Del Peak 25(16q24.3) mutation analysis"
[1] 3
  DEL PEAK 25(16Q24.3) MUTATED DEL PEAK 25(16Q24.3) WILD-TYPE 
                            44                             94 
  DEL PEAK 25(16Q24.3) MUTATED DEL PEAK 25(16Q24.3) WILD-TYPE 
                            44                             94 
[1] "Del Peak 26(17q21.31) mutation analysis"
[1] 3
  DEL PEAK 26(17Q21.31) MUTATED DEL PEAK 26(17Q21.31) WILD-TYPE 
                             29                             109 
  DEL PEAK 26(17Q21.31) MUTATED DEL PEAK 26(17Q21.31) WILD-TYPE 
                             29                             109 
[1] "Del Peak 27(19p13.3) mutation analysis"
[1] 3
  DEL PEAK 27(19P13.3) MUTATED DEL PEAK 27(19P13.3) WILD-TYPE 
                            41                             97 
  DEL PEAK 27(19P13.3) MUTATED DEL PEAK 27(19P13.3) WILD-TYPE 
                            41                             97 
[1] "Del Peak 28(22q12.1) mutation analysis"
[1] 3
  DEL PEAK 28(22Q12.1) MUTATED DEL PEAK 28(22Q12.1) WILD-TYPE 
                            17                            121 
  DEL PEAK 28(22Q12.1) MUTATED DEL PEAK 28(22Q12.1) WILD-TYPE 
                            17                            121 
[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 138 columns.

[1] "Batch" "10"   
[1] "Last Follow UP"
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-DA-A1HV 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A1NK TCGA-EB-A24C 
          NA           NA           NA           NA           NA           NA 
TCGA-EB-A24D TCGA-EB-A299 TCGA-EB-A3HV 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-A1ZN TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FW-A3I3 TCGA-GF-A2C7 
          NA           NA           NA           NA            6           NA 
TCGA-GN-A262 TCGA-GN-A263 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        3664           NA           NA         2577           NA           NA 
TCGA-GN-A268 TCGA-GN-A269 TCGA-GN-A26A TCGA-GN-A26C TCGA-GN-A26D TCGA-IH-A3EA 
          NA           NA           NA           NA         1204           NA 
Variable 1:'AGE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=11,	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=5,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'BATCH.NUMBER':	nDistinctValues=7,	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 138 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=18, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1p36.11) mutation analysis
D1V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK  1(1P36.11) WILD-TYPE"   "AMP PEAK  1(1P36.11) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK  1(1P36.11) WILD-TYPE"   "AMP PEAK  1(1P36.11) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK  1(1P36.11) WILD-TYPE"   "AMP PEAK  1(1P36.11) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  1(1P36.11) WILD-TYPE" "AMP PEAK  1(1P36.11) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK  1(1P36.11) MUTATED" "AMP PEAK  1(1P36.11) WILD-TYPE" 
[1] "hr=" "2.9"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  1(1P36.11) MUTATED     19    8
  AMP PEAK  1(1P36.11) WILD-TYPE   73   38
        clus
vv       AMP PEAK  1(1P36.11) MUTATED AMP PEAK  1(1P36.11) WILD-TYPE
  FEMALE                            8                             38
  MALE                             19                             73

Clustering(2) Variable = Amp Peak  2(1p12) mutation analysis
D2V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  2(1P12) WILD-TYPE"   "AMP PEAK  2(1P12) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  2(1P12) MUTATED" "AMP PEAK  2(1P12) WILD-TYPE" 
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1P12) MUTATED     27   13
  AMP PEAK  2(1P12) WILD-TYPE   65   33
        clus
vv       AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  FEMALE                        13                          33
  MALE                          27                          65

Clustering(3) Variable = Amp Peak  3(1q44) mutation analysis
D3V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  3(1Q44) WILD-TYPE" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  3(1Q44) MUTATED" "AMP PEAK  3(1Q44) WILD-TYPE" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  3(1Q44) WILD-TYPE"   "AMP PEAK  3(1Q44) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  3(1Q44) MUTATED"   "AMP PEAK  3(1Q44) MUTATED" 
[1] "hr=" "3"  
D3V2, continuous
D3V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(1Q44) MUTATED     46   27
  AMP PEAK  3(1Q44) WILD-TYPE   46   19
        clus
vv       AMP PEAK  3(1Q44) MUTATED AMP PEAK  3(1Q44) WILD-TYPE
  FEMALE                        27                          19
  MALE                          46                          46

Clustering(4) Variable = Amp Peak  4(3p13) mutation analysis
D4V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK  4(3P13) MUTATED"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  4(3P13) MUTATED" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK  4(3P13) MUTATED"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  4(3P13) MUTATED" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK  4(3P13) MUTATED"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  4(3P13) WILD-TYPE"   "AMP PEAK  4(3P13) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  4(3P13) WILD-TYPE" "AMP PEAK  4(3P13) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK  4(3P13) MUTATED" "AMP PEAK  4(3P13) WILD-TYPE" 
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3P13) MUTATED     18   13
  AMP PEAK  4(3P13) WILD-TYPE   74   33
        clus
vv       AMP PEAK  4(3P13) MUTATED AMP PEAK  4(3P13) WILD-TYPE
  FEMALE                        13                          33
  MALE                          18                          74

Clustering(5) Variable = Amp Peak  5(4q12) mutation analysis
D5V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"AMP PEAK  5(4Q12) WILD-TYPE" "AMP PEAK  5(4Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  5(4Q12) WILD-TYPE"   "AMP PEAK  5(4Q12) MUTATED" 
[1] "hr=" "1.8"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     14   10
  AMP PEAK  5(4Q12) WILD-TYPE   78   36
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        10                          36
  MALE                          14                          78

Clustering(6) Variable = Amp Peak  6(5p15.33) mutation analysis
D6V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK  6(5P15.33) MUTATED" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK  6(5P15.33) WILD-TYPE" "AMP PEAK  6(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK  6(5P15.33) WILD-TYPE"   "AMP PEAK  6(5P15.33) MUTATED" 
[1] "hr=" "3.7"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     26   14
  AMP PEAK  6(5P15.33) WILD-TYPE   66   32
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           14                             32
  MALE                             26                             66

Clustering(7) Variable = Amp Peak  7(5q35.3) mutation analysis
D7V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  7(5Q35.3) MUTATED" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  7(5Q35.3) MUTATED" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  7(5Q35.3) WILD-TYPE"   "AMP PEAK  7(5Q35.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  7(5Q35.3) MUTATED" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  7(5Q35.3) WILD-TYPE" "AMP PEAK  7(5Q35.3) WILD-TYPE" 
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.3) MUTATED      8    8
  AMP PEAK  7(5Q35.3) WILD-TYPE   84   38
        clus
vv       AMP PEAK  7(5Q35.3) MUTATED AMP PEAK  7(5Q35.3) WILD-TYPE
  FEMALE                           8                            38
  MALE                             8                            84

Clustering(8) Variable = Amp Peak  8(6p25.1) mutation analysis
D8V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  8(6P25.1) MUTATED" "AMP PEAK  8(6P25.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  8(6P25.1) MUTATED" "AMP PEAK  8(6P25.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK  8(6P25.1) MUTATED" "AMP PEAK  8(6P25.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK  8(6P25.1) MUTATED"   "AMP PEAK  8(6P25.1) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK  8(6P25.1) WILD-TYPE"   "AMP PEAK  8(6P25.1) MUTATED" 
[1] "hr=" "3.4"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P25.1) MUTATED     53   27
  AMP PEAK  8(6P25.1) WILD-TYPE   39   19
        clus
vv       AMP PEAK  8(6P25.1) MUTATED AMP PEAK  8(6P25.1) WILD-TYPE
  FEMALE                          27                            19
  MALE                            53                            39

Clustering(9) Variable = Amp Peak  9(6q12) mutation analysis
D9V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(6Q12) MUTATED"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(6Q12) MUTATED"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"AMP PEAK  9(6Q12) WILD-TYPE"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(6Q12) MUTATED"   "AMP PEAK  9(6Q12) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK  9(6Q12) MUTATED" "AMP PEAK  9(6Q12) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"AMP PEAK  9(6Q12) WILD-TYPE" "AMP PEAK  9(6Q12) WILD-TYPE" 
[1] "hr=" "2.1"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     20    9
  AMP PEAK  9(6Q12) WILD-TYPE   72   37
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                         9                          37
  MALE                          20                          72

Clustering(10) Variable = Amp Peak 10(7p22.3) mutation analysis
D10V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 10(7P22.3) MUTATED" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 10(7P22.3) MUTATED" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 10(7P22.3) WILD-TYPE" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 10(7P22.3) MUTATED" "AMP PEAK 10(7P22.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 10(7P22.3) WILD-TYPE"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 10(7P22.3) MUTATED"   "AMP PEAK 10(7P22.3) MUTATED" 
[1] "hr=" "3.4"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P22.3) MUTATED     54   27
  AMP PEAK 10(7P22.3) WILD-TYPE   38   19
        clus
vv       AMP PEAK 10(7P22.3) MUTATED AMP PEAK 10(7P22.3) WILD-TYPE
  FEMALE                          27                            19
  MALE                            54                            38

Clustering(11) Variable = Amp Peak 11(7q34) mutation analysis
D11V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK 11(7Q34) MUTATED" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK 11(7Q34) MUTATED" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"AMP PEAK 11(7Q34) WILD-TYPE" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "AMP PEAK 11(7Q34) MUTATED" "AMP PEAK 11(7Q34) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"AMP PEAK 11(7Q34) WILD-TYPE"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
  "AMP PEAK 11(7Q34) MUTATED"   "AMP PEAK 11(7Q34) MUTATED" 
[1] "hr=" "1.8"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 11(7Q34) MUTATED     53   32
  AMP PEAK 11(7Q34) WILD-TYPE   39   14
        clus
vv       AMP PEAK 11(7Q34) MUTATED AMP PEAK 11(7Q34) WILD-TYPE
  FEMALE                        32                          14
  MALE                          53                          39

Clustering(12) Variable = Amp Peak 12(8q11.22) mutation analysis
D12V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 12(8Q11.22) WILD-TYPE" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 12(8Q11.22) WILD-TYPE" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 12(8Q11.22) WILD-TYPE" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 12(8Q11.22) MUTATED" "AMP PEAK 12(8Q11.22) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 12(8Q11.22) WILD-TYPE"   "AMP PEAK 12(8Q11.22) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 12(8Q11.22) MUTATED"   "AMP PEAK 12(8Q11.22) MUTATED" 
[1] "hr=" "2.9"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q11.22) MUTATED     43   17
  AMP PEAK 12(8Q11.22) WILD-TYPE   49   29
        clus
vv       AMP PEAK 12(8Q11.22) MUTATED AMP PEAK 12(8Q11.22) WILD-TYPE
  FEMALE                           17                             29
  MALE                             43                             49

Clustering(13) Variable = Amp Peak 13(8q24.3) mutation analysis
D13V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "AMP PEAK 13(8Q24.3) MUTATED"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "AMP PEAK 13(8Q24.3) MUTATED"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "AMP PEAK 13(8Q24.3) MUTATED"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 13(8Q24.3) WILD-TYPE" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK 13(8Q24.3) MUTATED" "AMP PEAK 13(8Q24.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"AMP PEAK 13(8Q24.3) WILD-TYPE"   "AMP PEAK 13(8Q24.3) MUTATED" 
[1] "hr=" "4.1"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(8Q24.3) MUTATED     49   21
  AMP PEAK 13(8Q24.3) WILD-TYPE   43   25
        clus
vv       AMP PEAK 13(8Q24.3) MUTATED AMP PEAK 13(8Q24.3) WILD-TYPE
  FEMALE                          21                            25
  MALE                            49                            43

Clustering(14) Variable = Amp Peak 14(9p24.1) mutation analysis
D14V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 14(9P24.1) WILD-TYPE"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 14(9P24.1) MUTATED"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 14(9P24.1) MUTATED" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 14(9P24.1) WILD-TYPE"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 14(9P24.1) MUTATED"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 14(9P24.1) MUTATED" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK 14(9P24.1) WILD-TYPE"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "AMP PEAK 14(9P24.1) MUTATED"   "AMP PEAK 14(9P24.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"AMP PEAK 14(9P24.1) WILD-TYPE" "AMP PEAK 14(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
  "AMP PEAK 14(9P24.1) MUTATED" "AMP PEAK 14(9P24.1) WILD-TYPE" 
[1] "hr=" "2.7"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P24.1) MUTATED      6    5
  AMP PEAK 14(9P24.1) WILD-TYPE   86   41
        clus
vv       AMP PEAK 14(9P24.1) MUTATED AMP PEAK 14(9P24.1) WILD-TYPE
  FEMALE                           5                            41
  MALE                             6                            86

Clustering(15) Variable = Amp Peak 15(11q13.3) mutation analysis
D15V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 15(11Q13.3) WILD-TYPE" "AMP PEAK 15(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 15(11Q13.3) WILD-TYPE"   "AMP PEAK 15(11Q13.3) MUTATED" 
[1] "hr=" "1.4"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     14    3
  AMP PEAK 15(11Q13.3) WILD-TYPE   78   43
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                            3                             43
  MALE                             14                             78

Clustering(16) Variable = Amp Peak 16(11q13.4) mutation analysis
D16V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 16(11Q13.4) MUTATED"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 16(11Q13.4) MUTATED"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 16(11Q13.4) MUTATED"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 16(11Q13.4) WILD-TYPE" "AMP PEAK 16(11Q13.4) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 16(11Q13.4) WILD-TYPE"   "AMP PEAK 16(11Q13.4) MUTATED" 
[1] "hr=" "2.3"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q13.4) MUTATED     13    3
  AMP PEAK 16(11Q13.4) WILD-TYPE   79   43
        clus
vv       AMP PEAK 16(11Q13.4) MUTATED AMP PEAK 16(11Q13.4) WILD-TYPE
  FEMALE                            3                             43
  MALE                             13                             79

Clustering(17) Variable = Amp Peak 17(12q15) mutation analysis
D17V1, survival
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
  "AMP PEAK 17(12Q15) MUTATED"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
  "AMP PEAK 17(12Q15) MUTATED"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"AMP PEAK 17(12Q15) WILD-TYPE" "AMP PEAK 17(12Q15) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
  "AMP PEAK 17(12Q15) MUTATED"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
"AMP PEAK 17(12Q15) WILD-TYPE"   "AMP PEAK 17(12Q15) MUTATED" 
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     11    6
  AMP PEAK 17(12Q15) WILD-TYPE   81   40
        clus
vv       AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  FEMALE                          6                           40
  MALE                           11                           81

Clustering(18) Variable = Amp Peak 18(13q31.3) mutation analysis
D18V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(13Q31.3) MUTATED"   "AMP PEAK 18(13Q31.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 18(13Q31.3) MUTATED" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 18(13Q31.3) WILD-TYPE" "AMP PEAK 18(13Q31.3) WILD-TYPE" 
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(13Q31.3) MUTATED     25   11
  AMP PEAK 18(13Q31.3) WILD-TYPE   67   35
        clus
vv       AMP PEAK 18(13Q31.3) MUTATED AMP PEAK 18(13Q31.3) WILD-TYPE
  FEMALE                           11                             35
  MALE                             25                             67

Clustering(19) Variable = Amp Peak 19(15q26.2) mutation analysis
D19V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 19(15Q26.2) MUTATED" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 19(15Q26.2) WILD-TYPE"   "AMP PEAK 19(15Q26.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 19(15Q26.2) WILD-TYPE" "AMP PEAK 19(15Q26.2) WILD-TYPE" 
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(15Q26.2) MUTATED     29   16
  AMP PEAK 19(15Q26.2) WILD-TYPE   63   30
        clus
vv       AMP PEAK 19(15Q26.2) MUTATED AMP PEAK 19(15Q26.2) WILD-TYPE
  FEMALE                           16                             30
  MALE                             29                             63

Clustering(20) Variable = Amp Peak 20(17q25.3) mutation analysis
D20V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 20(17Q25.3) MUTATED" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 20(17Q25.3) WILD-TYPE" "AMP PEAK 20(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"AMP PEAK 20(17Q25.3) WILD-TYPE"   "AMP PEAK 20(17Q25.3) MUTATED" 
[1] "hr=" "2.3"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q25.3) MUTATED     38   16
  AMP PEAK 20(17Q25.3) WILD-TYPE   54   30
        clus
vv       AMP PEAK 20(17Q25.3) MUTATED AMP PEAK 20(17Q25.3) WILD-TYPE
  FEMALE                           16                             30
  MALE                             38                             54

Clustering(21) Variable = Amp Peak 21(19p13.2) mutation analysis
D21V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"AMP PEAK 21(19P13.2) WILD-TYPE"   "AMP PEAK 21(19P13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 21(19P13.2) WILD-TYPE" "AMP PEAK 21(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 21(19P13.2) MUTATED" "AMP PEAK 21(19P13.2) WILD-TYPE" 
[1] "hr=" "1.6"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     18    7
  AMP PEAK 21(19P13.2) WILD-TYPE   74   39
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  FEMALE                            7                             39
  MALE                             18                             74

Clustering(22) Variable = Amp Peak 22(20q13.2) mutation analysis
D22V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 22(20Q13.2) WILD-TYPE"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 22(20Q13.2) WILD-TYPE"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 22(20Q13.2) WILD-TYPE" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 22(20Q13.2) WILD-TYPE"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 22(20Q13.2) MUTATED" "AMP PEAK 22(20Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 22(20Q13.2) MUTATED"   "AMP PEAK 22(20Q13.2) MUTATED" 
[1] "hr=" "1"  
D22V2, continuous
D22V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(20Q13.2) MUTATED     51   21
  AMP PEAK 22(20Q13.2) WILD-TYPE   41   25
        clus
vv       AMP PEAK 22(20Q13.2) MUTATED AMP PEAK 22(20Q13.2) WILD-TYPE
  FEMALE                           21                             25
  MALE                             51                             41

Clustering(23) Variable = Amp Peak 23(22q13.2) mutation analysis
D23V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 23(22Q13.2) WILD-TYPE" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 23(22Q13.2) WILD-TYPE" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"AMP PEAK 23(22Q13.2) WILD-TYPE" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
  "AMP PEAK 23(22Q13.2) MUTATED" "AMP PEAK 23(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"AMP PEAK 23(22Q13.2) WILD-TYPE"   "AMP PEAK 23(22Q13.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
  "AMP PEAK 23(22Q13.2) MUTATED"   "AMP PEAK 23(22Q13.2) MUTATED" 
[1] "hr=" "2"  
D23V2, continuous
D23V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(22Q13.2) MUTATED     42   21
  AMP PEAK 23(22Q13.2) WILD-TYPE   50   25
        clus
vv       AMP PEAK 23(22Q13.2) MUTATED AMP PEAK 23(22Q13.2) WILD-TYPE
  FEMALE                           21                             25
  MALE                             42                             50

Clustering(24) Variable = Del Peak  1(1p36.31) mutation analysis
D24V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
[1] "hr=" "1.5"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     22   12
  DEL PEAK  1(1P36.31) WILD-TYPE   70   34
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           12                             34
  MALE                             22                             70

Clustering(25) Variable = Del Peak  2(1p22.1) mutation analysis
D25V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
[1] "hr=" "4.1"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED     19   13
  DEL PEAK  2(1P22.1) WILD-TYPE   73   33
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                          13                            33
  MALE                            19                            73

Clustering(26) Variable = Del Peak  3(2q37.3) mutation analysis
D26V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
[1] "hr=" "1.9"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED     22   14
  DEL PEAK  3(2Q37.3) WILD-TYPE   70   32
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                          14                            32
  MALE                            22                            70

Clustering(27) Variable = Del Peak  4(3q22.1) mutation analysis
D27V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  4(3Q22.1) MUTATED" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3Q22.1) MUTATED"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  4(3Q22.1) MUTATED" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3Q22.1) MUTATED"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK  4(3Q22.1) MUTATED" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  4(3Q22.1) WILD-TYPE"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3Q22.1) MUTATED"   "DEL PEAK  4(3Q22.1) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  4(3Q22.1) WILD-TYPE" "DEL PEAK  4(3Q22.1) WILD-TYPE" 
[1] "hr=" "1.7"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q22.1) MUTATED     11    8
  DEL PEAK  4(3Q22.1) WILD-TYPE   81   38
        clus
vv       DEL PEAK  4(3Q22.1) MUTATED DEL PEAK  4(3Q22.1) WILD-TYPE
  FEMALE                           8                            38
  MALE                            11                            81

Clustering(28) Variable = Del Peak  5(4p16.3) mutation analysis
D28V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  5(4P16.3) MUTATED" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  5(4P16.3) MUTATED" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  5(4P16.3) MUTATED" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4P16.3) WILD-TYPE"   "DEL PEAK  5(4P16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  5(4P16.3) WILD-TYPE" "DEL PEAK  5(4P16.3) WILD-TYPE" 
[1] "hr=" "1.7"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4P16.3) MUTATED     16   12
  DEL PEAK  5(4P16.3) WILD-TYPE   76   34
        clus
vv       DEL PEAK  5(4P16.3) MUTATED DEL PEAK  5(4P16.3) WILD-TYPE
  FEMALE                          12                            34
  MALE                            16                            76

Clustering(29) Variable = Del Peak  6(4q34.3) mutation analysis
D29V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  6(4Q34.3) MUTATED" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  6(4Q34.3) WILD-TYPE"   "DEL PEAK  6(4Q34.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  6(4Q34.3) WILD-TYPE" "DEL PEAK  6(4Q34.3) WILD-TYPE" 
[1] "hr=" "2.1"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     20   16
  DEL PEAK  6(4Q34.3) WILD-TYPE   72   30
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          16                            30
  MALE                            20                            72

Clustering(30) Variable = Del Peak  7(5q11.2) mutation analysis
D30V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  7(5Q11.2) MUTATED" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(5Q11.2) MUTATED"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  7(5Q11.2) MUTATED" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(5Q11.2) MUTATED"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  7(5Q11.2) MUTATED" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  7(5Q11.2) WILD-TYPE"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(5Q11.2) MUTATED"   "DEL PEAK  7(5Q11.2) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  7(5Q11.2) WILD-TYPE" "DEL PEAK  7(5Q11.2) WILD-TYPE" 
[1] "hr=" "1.6"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(5Q11.2) MUTATED     26   15
  DEL PEAK  7(5Q11.2) WILD-TYPE   66   31
        clus
vv       DEL PEAK  7(5Q11.2) MUTATED DEL PEAK  7(5Q11.2) WILD-TYPE
  FEMALE                          15                            31
  MALE                            26                            66

Clustering(31) Variable = Del Peak  8(5q31.3) mutation analysis
D31V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  8(5Q31.3) MUTATED"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  8(5Q31.3) MUTATED"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  8(5Q31.3) WILD-TYPE"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  8(5Q31.3) MUTATED"   "DEL PEAK  8(5Q31.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
  "DEL PEAK  8(5Q31.3) MUTATED" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  8(5Q31.3) WILD-TYPE" "DEL PEAK  8(5Q31.3) WILD-TYPE" 
[1] "hr=" "2.4"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q31.3) MUTATED     37   19
  DEL PEAK  8(5Q31.3) WILD-TYPE   55   27
        clus
vv       DEL PEAK  8(5Q31.3) MUTATED DEL PEAK  8(5Q31.3) WILD-TYPE
  FEMALE                          19                            27
  MALE                            37                            55

Clustering(32) Variable = Del Peak  9(6q16.3) mutation analysis
D32V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  9(6Q16.3) MUTATED" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  9(6Q16.3) MUTATED"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  9(6Q16.3) MUTATED" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  9(6Q16.3) MUTATED"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK  9(6Q16.3) MUTATED" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  9(6Q16.3) MUTATED"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK  9(6Q16.3) WILD-TYPE"   "DEL PEAK  9(6Q16.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK  9(6Q16.3) WILD-TYPE" "DEL PEAK  9(6Q16.3) WILD-TYPE" 
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q16.3) MUTATED     50   31
  DEL PEAK  9(6Q16.3) WILD-TYPE   42   15
        clus
vv       DEL PEAK  9(6Q16.3) MUTATED DEL PEAK  9(6Q16.3) WILD-TYPE
  FEMALE                          31                            15
  MALE                            50                            42

Clustering(33) Variable = Del Peak 10(6q26) mutation analysis
D33V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 10(6Q26) MUTATED" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 10(6Q26) MUTATED" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 10(6Q26) MUTATED" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 10(6Q26) MUTATED"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 10(6Q26) WILD-TYPE"   "DEL PEAK 10(6Q26) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 10(6Q26) WILD-TYPE" "DEL PEAK 10(6Q26) WILD-TYPE" 
[1] "hr=" "2.2"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     51   31
  DEL PEAK 10(6Q26) WILD-TYPE   41   15
        clus
vv       DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  FEMALE                        31                          15
  MALE                          51                          41

Clustering(34) Variable = Del Peak 11(6q27) mutation analysis
D34V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
[1] "hr=" "2.2"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q27) MUTATED     50   32
  DEL PEAK 11(6Q27) WILD-TYPE   42   14
        clus
vv       DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  FEMALE                        32                          14
  MALE                          50                          42

Clustering(35) Variable = Del Peak 12(9p23) mutation analysis
D35V1, survival
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A19D                  TCGA-ER-A19F 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19N 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-FW-A3I3                  TCGA-GN-A262 
"DEL PEAK 12(9P23) WILD-TYPE" "DEL PEAK 12(9P23) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A264 
  "DEL PEAK 12(9P23) MUTATED"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A265                  TCGA-GN-A266 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A269                  TCGA-GN-A26A 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
                 TCGA-GN-A26C                  TCGA-GN-A26D 
"DEL PEAK 12(9P23) WILD-TYPE"   "DEL PEAK 12(9P23) MUTATED" 
[1] "hr=" "2.2"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(9P23) MUTATED     57   35
  DEL PEAK 12(9P23) WILD-TYPE   35   11
        clus
vv       DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE
  FEMALE                        35                          11
  MALE                          57                          35

Clustering(36) Variable = Del Peak 13(9p21.3) mutation analysis
D36V1, survival
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 13(9P21.3) WILD-TYPE" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK 13(9P21.3) MUTATED" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 13(9P21.3) WILD-TYPE" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK 13(9P21.3) MUTATED" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A19D                    TCGA-ER-A19F 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19N 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 13(9P21.3) WILD-TYPE" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-FW-A3I3                    TCGA-GN-A262 
  "DEL PEAK 13(9P21.3) MUTATED" "DEL PEAK 13(9P21.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A264 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A265                    TCGA-GN-A266 
  "DEL PEAK 13(9P21.3) MUTATED"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A269                    TCGA-GN-A26A 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-GN-A26D 
"DEL PEAK 13(9P21.3) WILD-TYPE"   "DEL PEAK 13(9P21.3) MUTATED" 
[1] "hr=" "1.5"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9P21.3) MUTATED     67   40
  DEL PEAK 13(9P21.3) WILD-TYPE   25    6
        clus
vv       DEL PEAK 13(9P21.3) MUTATED DEL PEAK 13(9P21.3) WILD-TYPE
  FEMALE                          40                             6
  MALE                            67                            25

Clustering(37) Variable = Del Peak 14(10p15.3) mutation analysis
D37V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(10P15.3) MUTATED"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(10P15.3) MUTATED"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 14(10P15.3) MUTATED" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(10P15.3) MUTATED"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 14(10P15.3) WILD-TYPE"   "DEL PEAK 14(10P15.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 14(10P15.3) WILD-TYPE" "DEL PEAK 14(10P15.3) WILD-TYPE" 
[1] "hr=" "1.4"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(10P15.3) MUTATED     45   28
  DEL PEAK 14(10P15.3) WILD-TYPE   47   18
        clus
vv       DEL PEAK 14(10P15.3) MUTATED DEL PEAK 14(10P15.3) WILD-TYPE
  FEMALE                           28                             18
  MALE                             45                             47

Clustering(38) Variable = Del Peak 15(10q23.31) mutation analysis
D38V1, survival
                     TCGA-ER-A19D                      TCGA-ER-A19F 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
[1] "hr=" "1"  
D38V2, continuous
D38V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     50   34
  DEL PEAK 15(10Q23.31) WILD-TYPE   42   12
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            34                              12
  MALE                              50                              42

Clustering(39) Variable = Del Peak 16(10q26.3) mutation analysis
D39V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 16(10Q26.3) MUTATED" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 16(10Q26.3) WILD-TYPE"   "DEL PEAK 16(10Q26.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 16(10Q26.3) WILD-TYPE" "DEL PEAK 16(10Q26.3) WILD-TYPE" 
[1] "hr=" "1.6"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10Q26.3) MUTATED     50   34
  DEL PEAK 16(10Q26.3) WILD-TYPE   42   12
        clus
vv       DEL PEAK 16(10Q26.3) MUTATED DEL PEAK 16(10Q26.3) WILD-TYPE
  FEMALE                           34                             12
  MALE                             50                             42

Clustering(40) Variable = Del Peak 17(11q23.3) mutation analysis
D40V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(11Q23.3) MUTATED"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 17(11Q23.3) WILD-TYPE"   "DEL PEAK 17(11Q23.3) MUTATED" 
[1] "hr=" "1.5"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11Q23.3) MUTATED     48   28
  DEL PEAK 17(11Q23.3) WILD-TYPE   44   18
        clus
vv       DEL PEAK 17(11Q23.3) MUTATED DEL PEAK 17(11Q23.3) WILD-TYPE
  FEMALE                           28                             18
  MALE                             48                             44

Clustering(41) Variable = Del Peak 18(12q24.33) mutation analysis
D41V1, survival
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 18(12Q24.33) MUTATED"   "DEL PEAK 18(12Q24.33) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 18(12Q24.33) WILD-TYPE" "DEL PEAK 18(12Q24.33) WILD-TYPE" 
[1] "hr=" "1.5"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 18(12Q24.33) MUTATED     20   11
  DEL PEAK 18(12Q24.33) WILD-TYPE   72   35
        clus
vv       DEL PEAK 18(12Q24.33) MUTATED DEL PEAK 18(12Q24.33) WILD-TYPE
  FEMALE                            11                              35
  MALE                              20                              72

Clustering(42) Variable = Del Peak 19(13q34) mutation analysis
D42V1, survival
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"DEL PEAK 19(13Q34) WILD-TYPE"   "DEL PEAK 19(13Q34) MUTATED" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
  "DEL PEAK 19(13Q34) MUTATED"   "DEL PEAK 19(13Q34) MUTATED" 
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"DEL PEAK 19(13Q34) WILD-TYPE"   "DEL PEAK 19(13Q34) MUTATED" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
  "DEL PEAK 19(13Q34) MUTATED"   "DEL PEAK 19(13Q34) MUTATED" 
                  TCGA-ER-A19D                   TCGA-ER-A19F 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19N 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-FW-A3I3                   TCGA-GN-A262 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A263                   TCGA-GN-A264 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A265                   TCGA-GN-A266 
"DEL PEAK 19(13Q34) WILD-TYPE"   "DEL PEAK 19(13Q34) MUTATED" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A269                   TCGA-GN-A26A 
"DEL PEAK 19(13Q34) WILD-TYPE" "DEL PEAK 19(13Q34) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-GN-A26D 
  "DEL PEAK 19(13Q34) MUTATED"   "DEL PEAK 19(13Q34) MUTATED" 
[1] "hr=" "2.3"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(13Q34) MUTATED     21   12
  DEL PEAK 19(13Q34) WILD-TYPE   71   34
        clus
vv       DEL PEAK 19(13Q34) MUTATED DEL PEAK 19(13Q34) WILD-TYPE
  FEMALE                         12                           34
  MALE                           21                           71

Clustering(43) Variable = Del Peak 20(14q32.2) mutation analysis
D43V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(14Q32.2) MUTATED"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(14Q32.2) MUTATED"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(14Q32.2) MUTATED"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 20(14Q32.2) WILD-TYPE"   "DEL PEAK 20(14Q32.2) MUTATED" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 20(14Q32.2) WILD-TYPE" "DEL PEAK 20(14Q32.2) WILD-TYPE" 
[1] "hr=" "1.5"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(14Q32.2) MUTATED     30   12
  DEL PEAK 20(14Q32.2) WILD-TYPE   62   34
        clus
vv       DEL PEAK 20(14Q32.2) MUTATED DEL PEAK 20(14Q32.2) WILD-TYPE
  FEMALE                           12                             34
  MALE                             30                             62

Clustering(44) Variable = Del Peak 21(15q13.3) mutation analysis
D44V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(15Q13.3) MUTATED" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 21(15Q13.3) WILD-TYPE" "DEL PEAK 21(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 21(15Q13.3) WILD-TYPE"   "DEL PEAK 21(15Q13.3) MUTATED" 
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(15Q13.3) MUTATED     23   12
  DEL PEAK 21(15Q13.3) WILD-TYPE   69   34
        clus
vv       DEL PEAK 21(15Q13.3) MUTATED DEL PEAK 21(15Q13.3) WILD-TYPE
  FEMALE                           12                             34
  MALE                             23                             69

Clustering(45) Variable = Del Peak 22(15q15.3) mutation analysis
D45V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 22(15Q15.3) MUTATED" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 22(15Q15.3) MUTATED" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 22(15Q15.3) MUTATED" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 22(15Q15.3) WILD-TYPE" "DEL PEAK 22(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 22(15Q15.3) WILD-TYPE"   "DEL PEAK 22(15Q15.3) MUTATED" 
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(15Q15.3) MUTATED     19   13
  DEL PEAK 22(15Q15.3) WILD-TYPE   73   33
        clus
vv       DEL PEAK 22(15Q15.3) MUTATED DEL PEAK 22(15Q15.3) WILD-TYPE
  FEMALE                           13                             33
  MALE                             19                             73

Clustering(46) Variable = Del Peak 23(16p13.3) mutation analysis
D46V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 23(16P13.3) MUTATED" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 23(16P13.3) MUTATED" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 23(16P13.3) MUTATED" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 23(16P13.3) WILD-TYPE" "DEL PEAK 23(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 23(16P13.3) WILD-TYPE"   "DEL PEAK 23(16P13.3) MUTATED" 
[1] "hr=" "2.9"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(16P13.3) MUTATED     11   12
  DEL PEAK 23(16P13.3) WILD-TYPE   81   34
        clus
vv       DEL PEAK 23(16P13.3) MUTATED DEL PEAK 23(16P13.3) WILD-TYPE
  FEMALE                           12                             34
  MALE                             11                             81

Clustering(47) Variable = Del Peak 24(16q12.1) mutation analysis
D47V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 24(16Q12.1) MUTATED"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 24(16Q12.1) MUTATED"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
  "DEL PEAK 24(16Q12.1) MUTATED"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 24(16Q12.1) WILD-TYPE" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 24(16Q12.1) MUTATED" "DEL PEAK 24(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 24(16Q12.1) WILD-TYPE"   "DEL PEAK 24(16Q12.1) MUTATED" 
[1] "hr=" "1.6"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(16Q12.1) MUTATED     28   17
  DEL PEAK 24(16Q12.1) WILD-TYPE   64   29
        clus
vv       DEL PEAK 24(16Q12.1) MUTATED DEL PEAK 24(16Q12.1) WILD-TYPE
  FEMALE                           17                             29
  MALE                             28                             64

Clustering(48) Variable = Del Peak 25(16q24.3) mutation analysis
D48V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 25(16Q24.3) MUTATED"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 25(16Q24.3) MUTATED" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 25(16Q24.3) MUTATED"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 25(16Q24.3) MUTATED" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 25(16Q24.3) WILD-TYPE" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 25(16Q24.3) MUTATED"   "DEL PEAK 25(16Q24.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
  "DEL PEAK 25(16Q24.3) MUTATED" "DEL PEAK 25(16Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 25(16Q24.3) WILD-TYPE"   "DEL PEAK 25(16Q24.3) MUTATED" 
[1] "hr=" "1"  
D48V2, continuous
D48V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16Q24.3) MUTATED     26   18
  DEL PEAK 25(16Q24.3) WILD-TYPE   66   28
        clus
vv       DEL PEAK 25(16Q24.3) MUTATED DEL PEAK 25(16Q24.3) WILD-TYPE
  FEMALE                           18                             28
  MALE                             26                             66

Clustering(49) Variable = Del Peak 26(17q21.31) mutation analysis
D49V1, survival
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 26(17Q21.31) MUTATED" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 26(17Q21.31) MUTATED" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A19D                      TCGA-ER-A19F 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19N 
  "DEL PEAK 26(17Q21.31) MUTATED" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-ER-A1A1                      TCGA-ER-A3ET 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-FW-A3I3                      TCGA-GN-A262 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A264 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A265                      TCGA-GN-A266 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 26(17Q21.31) MUTATED"   "DEL PEAK 26(17Q21.31) MUTATED" 
                     TCGA-GN-A269                      TCGA-GN-A26A 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-GN-A26D 
"DEL PEAK 26(17Q21.31) WILD-TYPE" "DEL PEAK 26(17Q21.31) WILD-TYPE" 
[1] "hr=" "2.4"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(17Q21.31) MUTATED     18   11
  DEL PEAK 26(17Q21.31) WILD-TYPE   74   35
        clus
vv       DEL PEAK 26(17Q21.31) MUTATED DEL PEAK 26(17Q21.31) WILD-TYPE
  FEMALE                            11                              35
  MALE                              18                              74

Clustering(50) Variable = Del Peak 27(19p13.3) mutation analysis
D50V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 27(19P13.3) WILD-TYPE"   "DEL PEAK 27(19P13.3) MUTATED" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
[1] "Remove cluster labels:"       "DEL PEAK 27(19P13.3) MUTATED"
clus
  DEL PEAK 27(19P13.3) MUTATED DEL PEAK 27(19P13.3) WILD-TYPE 
                             2                             16 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A263 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A266                     TCGA-GN-A267 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
D50V2, continuous
[1] "Remove cluster labels:"       "DEL PEAK 27(19P13.3) MUTATED"
clus
  DEL PEAK 27(19P13.3) MUTATED DEL PEAK 27(19P13.3) WILD-TYPE 
                             2                             17 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A19O                     TCGA-ER-A1A1 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-ER-A3ET                     TCGA-FW-A3I3 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A269 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26C 
"DEL PEAK 27(19P13.3) WILD-TYPE" "DEL PEAK 27(19P13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
"DEL PEAK 27(19P13.3) WILD-TYPE" 
D50V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(19P13.3) MUTATED     23   18
  DEL PEAK 27(19P13.3) WILD-TYPE   69   28
        clus
vv       DEL PEAK 27(19P13.3) MUTATED DEL PEAK 27(19P13.3) WILD-TYPE
  FEMALE                           18                             28
  MALE                             23                             69

Clustering(51) Variable = Del Peak 28(22q12.1) mutation analysis
D51V1, survival
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 28(22Q12.1) MUTATED" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 28(22Q12.1) WILD-TYPE"   "DEL PEAK 28(22Q12.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 28(22Q12.1) MUTATED" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 28(22Q12.1) WILD-TYPE"   "DEL PEAK 28(22Q12.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19D                     TCGA-ER-A19F 
  "DEL PEAK 28(22Q12.1) MUTATED" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19N 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A266 
"DEL PEAK 28(22Q12.1) WILD-TYPE"   "DEL PEAK 28(22Q12.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
[1] "Remove cluster labels:"       "DEL PEAK 28(22Q12.1) MUTATED"
clus
  DEL PEAK 28(22Q12.1) MUTATED DEL PEAK 28(22Q12.1) WILD-TYPE 
                             2                             16 
                    TCGA-ER-A19F                     TCGA-ER-A19L 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A3ET                     TCGA-FW-A3I3 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A263 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A269                     TCGA-GN-A26A 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-GN-A26D 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
D51V2, continuous
[1] "Remove cluster labels:"       "DEL PEAK 28(22Q12.1) MUTATED"
clus
  DEL PEAK 28(22Q12.1) MUTATED DEL PEAK 28(22Q12.1) WILD-TYPE 
                             2                             17 
                    TCGA-ER-A19F                     TCGA-ER-A19L 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A19O 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-FW-A3I3                     TCGA-GN-A262 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A264 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A265                     TCGA-GN-A267 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A268                     TCGA-GN-A269 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26C 
"DEL PEAK 28(22Q12.1) WILD-TYPE" "DEL PEAK 28(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26D 
"DEL PEAK 28(22Q12.1) WILD-TYPE" 
D51V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(22Q12.1) MUTATED     11    6
  DEL PEAK 28(22Q12.1) WILD-TYPE   81   40
        clus
vv       DEL PEAK 28(22Q12.1) MUTATED DEL PEAK 28(22Q12.1) WILD-TYPE
  FEMALE                            6                             40
  MALE                             11                             81
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
