
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.48.4103/CNV2ClinicalAnalysis_nozzle_onlysig_focal.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.48.4103/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/404111/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_LN/3215666/SKCM-Regional_LN.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-Regional_LN", "-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-Regional_LN"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=116, in cluster file=112, common to both=112
[1]  39 112
[1] "Amp Peak  1(1p12) mutation analysis"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         32                          80 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         32                          80 
[1] "Amp Peak  2(1q44) mutation analysis"
[1] 3
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         54                          58 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         54                          58 
[1] "Amp Peak  3(3p13) mutation analysis"
[1] 3
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         24                          88 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         24                          88 
[1] "Amp Peak  4(5p15.33) mutation analysis"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            32                             80 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            32                             80 
[1] "Amp Peak  5(5q35.3) mutation analysis"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           13                            99 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                           13                            99 
[1] "Amp Peak  6(6p25.1) mutation analysis"
[1] 3
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                           61                            51 
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                           61                            51 
[1] "Amp Peak  7(6q12) mutation analysis"
[1] 3
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         23                          89 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         23                          89 
[1] "Amp Peak  8(7p22.1) mutation analysis"
[1] 3
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           60                            52 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           60                            52 
[1] "Amp Peak  9(7q34) mutation analysis"
[1] 3
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                         62                          50 
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                         62                          50 
[1] "Amp Peak 10(8q11.21) mutation analysis"
[1] 3
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                            41                             71 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                            41                             71 
[1] "Amp Peak 11(8q24.21) mutation analysis"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            50                             62 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            50                             62 
[1] "Amp Peak 12(9p24.1) mutation analysis"
[1] 3
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            5                           107 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            5                           107 
[1] "Amp Peak 13(11q13.3) mutation analysis"
[1] 3
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            19                             93 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            19                             93 
[1] "Amp Peak 14(12q14.1) mutation analysis"
[1] 3
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            20                             92 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            20                             92 
[1] "Amp Peak 15(15q26.2) mutation analysis"
[1] 3
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                            43                             69 
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                            43                             69 
[1] "Amp Peak 16(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                            44                             68 
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                            44                             68 
[1] "Amp Peak 17(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                            19                             93 
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                            19                             93 
[1] "Amp Peak 18(22q13.2) mutation analysis"
[1] 3
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                            48                             64 
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                            48                             64 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            27                             85 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            27                             85 
[1] "Del Peak  2(1p21.3) mutation analysis"
[1] 3
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           30                            82 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           30                            82 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           21                            91 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           21                            91 
[1] "Del Peak  4(3p24.3) mutation analysis"
[1] 3
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           17                            95 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           17                            95 
[1] "Del Peak  5(4q34.3) mutation analysis"
[1] 3
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           23                            89 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           23                            89 
[1] "Del Peak  6(5q31.3) mutation analysis"
[1] 3
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                           45                            67 
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                           45                            67 
[1] "Del Peak  7(6q25.3) mutation analysis"
[1] 3
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                           67                            45 
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                           67                            45 
[1] "Del Peak  8(6q26) mutation analysis"
[1] 3
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         63                          49 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         63                          49 
[1] "Del Peak  9(8p23.3) mutation analysis"
[1] 3
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                           29                            83 
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                           29                            83 
[1] "Del Peak 10(9p23) mutation analysis"
[1] 3
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                         75                          37 
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                         75                          37 
[1] "Del Peak 11(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           86                            26 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           86                            26 
[1] "Del Peak 12(10p15.3) mutation analysis"
[1] 3
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            55                             57 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            55                             57 
[1] "Del Peak 13(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                             64                              48 
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                             64                              48 
[1] "Del Peak 14(11q23.1) mutation analysis"
[1] 3
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                            61                             51 
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                            61                             51 
[1] "Del Peak 15(12q24.33) mutation analysis"
[1] 3
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                             21                              91 
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                             21                              91 
[1] "Del Peak 16(13q34) mutation analysis"
[1] 3
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                          31                           81 
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                          31                           81 
[1] "Del Peak 17(15q13.3) mutation analysis"
[1] 3
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                            25                             87 
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                            25                             87 
[1] "Del Peak 18(15q15.3) mutation analysis"
[1] 3
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                            26                             86 
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                            26                             86 
[1] "Del Peak 19(16p13.3) mutation analysis"
[1] 3
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                            22                             90 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                            22                             90 
[1] "Del Peak 20(16q12.1) mutation analysis"
[1] 3
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                            38                             74 
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                            38                             74 
[1] "Del Peak 21(16q24.2) mutation analysis"
[1] 3
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                            43                             69 
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                            43                             69 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 112 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
          NA           NA         3004           NA           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3CF TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
          NA           NA           NA           NA          122           87 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
        1484           NA         1555           NA          680           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
         534          451           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
          NA          156         1155           NA         1175          134 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
          NA           NA          366          269          304          197 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
          NA           NA          769          727          272           NA 
TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
          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-A3AH TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
          NA           NA           NA           NA           NA         1303 
TCGA-ER-A19O TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1Z4 
          NA         2386          181         2195           NA           NA 
TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GN-A264 
          NA           NA          328           31           NA           NA 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        2577           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "GENDER"                "DISTANT.METASTASIS"   
[4] "LYMPH.NODE.METASTASIS" "TUMOR.STAGECODE"       "NEOPLASM.DISEASESTAGE"
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  4   4  10   3  12  12   4   3  13   7   1   5  15   1   8 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 112 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=10, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1p12) mutation analysis
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1P12) MUTATED    6 13
  AMP PEAK  1(1P12) WILD-TYPE 21 19
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         19                          40 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                         13                          19 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A3F3 
       16.47        10.26        11.41         4.01         2.86         7.00 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.12        12.20         4.27        37.97        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29X TCGA-ER-A19L TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 
        1.08         8.09        12.99         5.95        72.16        31.33 
TCGA-GN-A267 
       16.21 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1HW 
        6.35        15.25        13.32        24.00        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        13.68        22.36        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        6.31         5.13         4.41         9.47        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        9.99         6.48        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 
       11.11         4.18        28.64        42.84        78.44        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        84.72        15.39        14.70 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                       1.08                        1.02 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      72.16                       98.76 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                     11.150                      14.765 
[1] "1.1 - 72.2 (11.2)" "1.0 - 98.8 (14.8)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" 
[1] "hr=" "1.9"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      9   23
  AMP PEAK  1(1P12) WILD-TYPE   26   54
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  FEMALE                         9                          26
  MALE                          23                          54
                             vv
clus                          M0 M1 M1B M1C
  AMP PEAK  1(1P12) MUTATED   27  0   0   1
  AMP PEAK  1(1P12) WILD-TYPE 71  1   2   0
D1V4, multiclass
     clus
vv    AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  M0                         27                          71
  M1                          0                           1
  M1B                         0                           2
  M1C                         1                           0
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  1(1P12) MUTATED   15  0   2   4  0   1   1   1  4  0
  AMP PEAK  1(1P12) WILD-TYPE 46  1   1   6  1   2   7   0  9  2
D1V5, multiclass
D1V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  1(1P12) MUTATED             0       3        2        3        4
  AMP PEAK  1(1P12) WILD-TYPE           1      12        5        8        9
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  1(1P12) MUTATED           1         2         0         0
  AMP PEAK  1(1P12) WILD-TYPE         4         3         2         4
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  1(1P12) MUTATED            3          3          6        1
  AMP PEAK  1(1P12) WILD-TYPE          0          7         12        2
D1V7, multiclass

Clustering(2) Variable = Amp Peak  2(1q44) mutation analysis
D2V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  2(1Q44) MUTATED   15 14
  AMP PEAK  2(1Q44) WILD-TYPE 12 18
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         29                          30 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         14                          18 
$`AMP PEAK  2(1Q44) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       16.47        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A3CE TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A3F3 TCGA-DA-A3F5 
       13.32         4.01         2.86        51.12         7.00        17.56 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        6.31         1.12         4.27        11.15        38.63         1.08 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       12.03         8.84         6.48        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A267 TCGA-GN-A26D 
       11.11         5.95        72.16        16.21        14.70 

$`AMP PEAK  2(1Q44) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
       32.55        22.55        10.26         6.35        15.25        24.00 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X 
       48.79        35.80        13.68        22.36        14.83        11.57 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29S 
       12.20         5.13        37.97         4.41         9.47         9.99 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.09        11.31         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       78.44        10.78         1.02        31.33        84.72        15.39 

  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                       1.08                        1.02 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                      98.76                       84.72 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                     11.410                      14.255 
[1] "1.1 - 98.8 (11.4)" "1.0 - 84.7 (14.3)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED     17   37
  AMP PEAK  2(1Q44) WILD-TYPE   18   40
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  FEMALE                        17                          18
  MALE                          37                          40
                             vv
clus                          M0 M1 M1B M1C
  AMP PEAK  2(1Q44) MUTATED   48  0   1   1
  AMP PEAK  2(1Q44) WILD-TYPE 50  1   1   0
D2V4, multiclass
     clus
vv    AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  M0                         48                          50
  M1                          0                           1
  M1B                         1                           1
  M1C                         1                           0
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  2(1Q44) MUTATED   28  0   2   7  0   2   1   1  8  2
  AMP PEAK  2(1Q44) WILD-TYPE 33  1   1   3  1   1   7   0  5  0
D2V5, multiclass
D2V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  2(1Q44) MUTATED             0       6        4        6        8
  AMP PEAK  2(1Q44) WILD-TYPE           1       9        3        5        5
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  2(1Q44) MUTATED           0         1         2         1
  AMP PEAK  2(1Q44) WILD-TYPE         5         4         0         3
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  2(1Q44) MUTATED            3          4         10        2
  AMP PEAK  2(1Q44) WILD-TYPE          0          6          8        1
D2V7, multiclass

Clustering(3) Variable = Amp Peak  3(3p13) mutation analysis
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(3P13) MUTATED    8 10
  AMP PEAK  3(3P13) WILD-TYPE 19 22
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         18                          41 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         10                          22 
$`AMP PEAK  3(3P13) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A3F5 
       22.55         8.38        11.41        13.32        35.80        17.56 
TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29T 
       14.83         5.13         4.41         1.08         8.84         6.48 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       12.99        28.64        72.16        31.33        84.72        15.39 

$`AMP PEAK  3(3P13) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J9 
       16.47        32.55        98.76        28.08        10.26        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
        6.35        15.25        24.00         4.01         2.86        48.79 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z 
       51.12        13.68        22.36         7.00        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        1.12        12.20         4.27        37.97        11.15        38.63 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.47        12.03         9.99         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       23.90         8.94        11.11         4.18        42.84        78.44 
TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A26D 
        5.95        10.78         1.02        16.21        14.70 

  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                       1.08                        1.02 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                      84.72                       98.76 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                     14.075                      12.030 
[1] "1.1 - 84.7 (14.1)" "1.0 - 98.8 (12.0)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  3(3P13) WILD-TYPE" 
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(3P13) MUTATED      9   15
  AMP PEAK  3(3P13) WILD-TYPE   26   62
        clus
vv       AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE
  FEMALE                         9                          26
  MALE                          15                          62
                             vv
clus                          M0 M1 M1B M1C
  AMP PEAK  3(3P13) MUTATED   21  0   0   0
  AMP PEAK  3(3P13) WILD-TYPE 77  1   2   1
D3V4, multiclass
     clus
vv    AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE
  M0                         21                          77
  M1                          0                           1
  M1B                         0                           2
  M1C                         0                           1
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  3(3P13) MUTATED   12  0   0   4  0   1   1   0  2  1
  AMP PEAK  3(3P13) WILD-TYPE 49  1   3   6  1   2   7   1 11  1
D3V5, multiclass
D3V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  3(3P13) MUTATED             0       4        3        2        2
  AMP PEAK  3(3P13) WILD-TYPE           1      11        4        9       11
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  3(3P13) MUTATED           0         1         0         1
  AMP PEAK  3(3P13) WILD-TYPE         5         4         2         3
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  3(3P13) MUTATED            0          3          4        0
  AMP PEAK  3(3P13) WILD-TYPE          3          7         14        3
D3V7, multiclass

Clustering(4) Variable = Amp Peak  4(5p15.33) mutation analysis
D4V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  4(5P15.33) MUTATED    8 11
  AMP PEAK  4(5P15.33) WILD-TYPE 19 21
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            19                             40 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            11                             21 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1I2 
       22.55         6.35        15.25        24.00        48.79        13.68 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29T 
        7.00        17.56         1.12        11.15        38.63         6.48 
TCGA-EE-A2A0 TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 
       11.31        28.64        42.84        72.16        31.33        84.72 
TCGA-GN-A26D 
       14.70 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
       21.14        11.41        13.32         4.01         2.86        35.80 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
       51.12        22.36        14.83        11.57         6.31        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        4.27         5.13        37.97         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
       12.03         8.84         9.99         8.09        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FR-A3YN 
        8.94        11.11         4.18        12.99        78.44         5.95 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        16.21        15.39 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          1.12                           1.02 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         17.56                          11.49 
[1] "1.1 - 84.7 (17.6)" "1.0 - 98.8 (11.5)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK  4(5P15.33) MUTATED" 
[1] "hr=" "1.4"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     11   21
  AMP PEAK  4(5P15.33) WILD-TYPE   24   56
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                           11                             24
  MALE                             21                             56
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK  4(5P15.33) MUTATED   24  0   1   0
  AMP PEAK  4(5P15.33) WILD-TYPE 74  1   1   1
D4V4, multiclass
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  M0                            24                             74
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  4(5P15.33) MUTATED   12  0   0   3  0   2   5   0  3  1
  AMP PEAK  4(5P15.33) WILD-TYPE 49  1   3   7  1   1   3   1 10  1
D4V5, multiclass
D4V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  4(5P15.33) MUTATED             0       2        1        2        5
  AMP PEAK  4(5P15.33) WILD-TYPE           1      13        6        9        8
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  4(5P15.33) MUTATED           1         0         1         0
  AMP PEAK  4(5P15.33) WILD-TYPE         4         5         1         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  4(5P15.33) MUTATED            0          5          6        0
  AMP PEAK  4(5P15.33) WILD-TYPE          3          5         12        3
D4V7, multiclass

Clustering(5) Variable = Amp Peak  5(5q35.3) mutation analysis
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(5Q35.3) MUTATED    3  2
  AMP PEAK  5(5Q35.3) WILD-TYPE 24 30
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                            54 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            2                            30 
$`AMP PEAK  5(5Q35.3) MUTATED`
TCGA-D3-A3CF TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19F 
       24.00         4.41         8.84         6.48        11.11 

$`AMP PEAK  5(5Q35.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.12        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29X 
       38.63         1.08         9.47        12.03         9.99         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L 
       11.31        25.28        23.90         8.94         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       28.64        42.84        78.44         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        31.33        84.72        16.21        15.39        14.70 

  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         4.41                          1.02 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        24.00                         98.76 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         8.84                         13.50 
[1] "4.4 - 24.0 (8.8)"  "1.0 - 98.8 (13.5)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  5(5Q35.3) MUTATED" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" 
[1] "hr=" "1.4"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      5    8
  AMP PEAK  5(5Q35.3) WILD-TYPE   30   69
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  FEMALE                           5                            30
  MALE                             8                            69
                               vv
clus                            M0 M1 M1B M1C
  AMP PEAK  5(5Q35.3) MUTATED   12  0   1   0
  AMP PEAK  5(5Q35.3) WILD-TYPE 86  1   1   1
D5V4, multiclass
     clus
vv    AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  M0                           12                            86
  M1                            0                             1
  M1B                           1                             1
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  5(5Q35.3) MUTATED    8  0   0   1  0   1   0   0  2  1
  AMP PEAK  5(5Q35.3) WILD-TYPE 53  1   3   9  1   2   8   1 11  1
D5V5, multiclass
D5V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  5(5Q35.3) MUTATED             0       1        2        1        2
  AMP PEAK  5(5Q35.3) WILD-TYPE           1      14        5       10       11
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  5(5Q35.3) MUTATED           1         0         0         0
  AMP PEAK  5(5Q35.3) WILD-TYPE         4         5         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  5(5Q35.3) MUTATED            0          0          2        0
  AMP PEAK  5(5Q35.3) WILD-TYPE          3         10         16        3
D5V7, multiclass

Clustering(6) Variable = Amp Peak  6(6p25.1) mutation analysis
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(6P25.1) MUTATED    8 20
  AMP PEAK  6(6P25.1) WILD-TYPE 19 12
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                           28                            31 
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                           20                            12 
$`AMP PEAK  6(6P25.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3C6 
       16.47        98.76        22.55         8.38        21.14        15.25 
TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 
       13.32        48.79        13.68         7.00         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       12.20         4.27        11.15         1.08        12.03         8.84 
TCGA-EE-A29S TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-FS-A4F9 
        9.99        11.11         4.18        28.64        42.84        10.78 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        16.21        15.39        14.70 

$`AMP PEAK  6(6P25.1) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CF 
       32.55        28.08        10.26        11.41         6.35        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F5 
        4.01         2.86        35.80        51.12        22.36        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       14.83        11.57         5.13        37.97        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.47         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FW-A3R5 
        8.94        12.99        78.44         5.95        72.16         1.02 
TCGA-GN-A265 
       84.72 

  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                         1.08                          1.02 
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                        98.76                         84.72 
  AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE 
                        12.76                         12.99 
[1] "1.1 - 98.8 (12.8)" "1.0 - 84.7 (13.0)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  6(6P25.1) WILD-TYPE"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK  6(6P25.1) WILD-TYPE" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  6(6P25.1) MUTATED" "AMP PEAK  6(6P25.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  6(6P25.1) MUTATED"   "AMP PEAK  6(6P25.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  6(6P25.1) MUTATED" 
[1] "hr=" "2.2"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(6P25.1) MUTATED     23   38
  AMP PEAK  6(6P25.1) WILD-TYPE   12   39
        clus
vv       AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE
  FEMALE                          23                            12
  MALE                            38                            39
                               vv
clus                            M0 M1 M1B M1C
  AMP PEAK  6(6P25.1) MUTATED   52  1   1   1
  AMP PEAK  6(6P25.1) WILD-TYPE 46  0   1   0
D6V4, multiclass
     clus
vv    AMP PEAK  6(6P25.1) MUTATED AMP PEAK  6(6P25.1) WILD-TYPE
  M0                           52                            46
  M1                            1                             0
  M1B                           1                             1
  M1C                           1                             0
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  6(6P25.1) MUTATED   34  0   3   4  0   3   4   1  7  0
  AMP PEAK  6(6P25.1) WILD-TYPE 27  1   0   6  1   0   4   0  6  2
D6V5, multiclass
D6V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  6(6P25.1) MUTATED             0       9        3        6        7
  AMP PEAK  6(6P25.1) WILD-TYPE           1       6        4        5        6
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  6(6P25.1) MUTATED           3         3         2         1
  AMP PEAK  6(6P25.1) WILD-TYPE         2         2         0         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  6(6P25.1) MUTATED            3          5          9        2
  AMP PEAK  6(6P25.1) WILD-TYPE          0          5          9        1
D6V7, multiclass

Clustering(7) Variable = Amp Peak  7(6q12) mutation analysis
D7V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  7(6Q12) MUTATED    3  7
  AMP PEAK  7(6Q12) WILD-TYPE 24 25
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                         10                          49 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                          7                          25 
$`AMP PEAK  7(6Q12) MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-DA-A1HV TCGA-EE-A181 TCGA-EE-A183 
       98.76         8.38        21.14        48.79         1.12        12.20 
TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       28.64        42.84        16.21        15.39 

$`AMP PEAK  7(6Q12) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD 
       16.47        32.55        28.08        22.55        10.26        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        6.35        15.25        13.32        24.00         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
       35.80        51.12        13.68        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
       14.83        11.57         6.31         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 
       23.90         8.94        11.11         4.18        12.99        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        5.95        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A26D 
       14.70 

  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                       1.12                        1.02 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                      98.76                       84.72 
  AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE 
                     18.675                      11.570 
[1] "1.1 - 98.8 (18.7)" "1.0 - 84.7 (11.6)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  7(6Q12) WILD-TYPE"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "AMP PEAK  7(6Q12) MUTATED" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
"AMP PEAK  7(6Q12) WILD-TYPE" "AMP PEAK  7(6Q12) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  7(6Q12) MUTATED"   "AMP PEAK  7(6Q12) MUTATED" 
                 TCGA-GN-A26D 
"AMP PEAK  7(6Q12) WILD-TYPE" 
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(6Q12) MUTATED      5   18
  AMP PEAK  7(6Q12) WILD-TYPE   30   59
        clus
vv       AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  FEMALE                         5                          30
  MALE                          18                          59
                             vv
clus                          M0 M1 M1B M1C
  AMP PEAK  7(6Q12) MUTATED   20  0   0   0
  AMP PEAK  7(6Q12) WILD-TYPE 78  1   2   1
D7V4, multiclass
     clus
vv    AMP PEAK  7(6Q12) MUTATED AMP PEAK  7(6Q12) WILD-TYPE
  M0                         20                          78
  M1                          0                           1
  M1B                         0                           2
  M1C                         0                           1
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  7(6Q12) MUTATED   14  0   3   0  0   1   1   0  1  0
  AMP PEAK  7(6Q12) WILD-TYPE 47  1   0  10  1   2   7   1 12  2
D7V5, multiclass
D7V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  7(6Q12) MUTATED             0       4        1        4        2
  AMP PEAK  7(6Q12) WILD-TYPE           1      11        6        7       11
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  7(6Q12) MUTATED           1         2         0         0
  AMP PEAK  7(6Q12) WILD-TYPE         4         3         2         4
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  7(6Q12) MUTATED            2          2          1        0
  AMP PEAK  7(6Q12) WILD-TYPE          1          8         17        3
D7V7, multiclass

Clustering(8) Variable = Amp Peak  8(7p22.1) mutation analysis
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(7P22.1) MUTATED   11 18
  AMP PEAK  8(7P22.1) WILD-TYPE 16 14
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           29                            30 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                           18                            14 
$`AMP PEAK  8(7P22.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D9-A3Z3 
       16.47        32.55        22.55        21.14        11.41         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-EE-A17Z TCGA-EE-A181 
       48.79        35.80        51.12        13.68         6.31         1.12 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19M TCGA-FR-A3YN 
        6.48        11.31         8.94         4.18        28.64         5.95 
TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       72.16        31.33        16.21        15.39        14.70 

$`AMP PEAK  8(7P22.1) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JK TCGA-D3-A3C6 
       98.76        28.08        10.26         8.38         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
       13.32        24.00         4.01        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29H 
       14.83        11.57        12.20         4.27         5.13         4.41 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F 
        8.84         9.99         8.09        25.28        23.90        11.11 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 
       12.99        42.84        78.44        10.78         1.02        84.72 

  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                         1.08                          1.02 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                        72.16                         98.76 
  AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE 
                       14.700                        11.885 
[1] "1.1 - 72.2 (14.7)" "1.0 - 98.8 (11.9)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK  8(7P22.1) WILD-TYPE"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK  8(7P22.1) WILD-TYPE" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "AMP PEAK  8(7P22.1) MUTATED" "AMP PEAK  8(7P22.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "AMP PEAK  8(7P22.1) MUTATED"   "AMP PEAK  8(7P22.1) MUTATED" 
                   TCGA-GN-A26D 
  "AMP PEAK  8(7P22.1) MUTATED" 
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(7P22.1) MUTATED     19   41
  AMP PEAK  8(7P22.1) WILD-TYPE   16   36
        clus
vv       AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  FEMALE                          19                            16
  MALE                            41                            36
                               vv
clus                            M0 M1 M1B M1C
  AMP PEAK  8(7P22.1) MUTATED   51  1   1   1
  AMP PEAK  8(7P22.1) WILD-TYPE 47  0   1   0
D8V4, multiclass
     clus
vv    AMP PEAK  8(7P22.1) MUTATED AMP PEAK  8(7P22.1) WILD-TYPE
  M0                           51                            47
  M1                            1                             0
  M1B                           1                             1
  M1C                           1                             0
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  8(7P22.1) MUTATED   33  0   2   7  0   2   2   1  6  2
  AMP PEAK  8(7P22.1) WILD-TYPE 28  1   1   3  1   1   6   0  7  0
D8V5, multiclass
D8V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  8(7P22.1) MUTATED             1       9        4        4        7
  AMP PEAK  8(7P22.1) WILD-TYPE           0       6        3        7        6
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  8(7P22.1) MUTATED           3         2         2         0
  AMP PEAK  8(7P22.1) WILD-TYPE         2         3         0         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  8(7P22.1) MUTATED            3          6          8        2
  AMP PEAK  8(7P22.1) WILD-TYPE          0          4         10        1
D8V7, multiclass

Clustering(9) Variable = Amp Peak  9(7q34) mutation analysis
D9V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  9(7Q34) MUTATED   15 18
  AMP PEAK  9(7Q34) WILD-TYPE 12 14
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                         33                          26 
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                         18                          14 
$`AMP PEAK  9(7Q34) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
       16.47        32.55        22.55        21.14        11.41        13.32 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F5 
        2.86        48.79        35.80        51.12        13.68        17.56 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       14.83         1.12        12.20        37.97        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 
        1.08         9.47        12.03         6.48        11.31         8.94 
TCGA-ER-A19J TCGA-ER-A19M TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 
        4.18        28.64         5.95        72.16        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       16.21        15.39        14.70 

$`AMP PEAK  9(7Q34) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JK TCGA-D3-A3C6 
       98.76        28.08        10.26         8.38         6.35        15.25 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z 
       24.00         4.01        22.36         7.00        11.57         6.31 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X 
        4.27         5.13        11.15         8.84         9.99         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
       25.28        23.90        11.11        12.99        42.84        78.44 
TCGA-FS-A4F9 TCGA-FW-A3R5 
       10.78         1.02 

  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                       1.08                        1.02 
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                      84.72                       98.76 
  AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE 
                     14.830                      10.945 
[1] "1.1 - 84.7 (14.8)" "1.0 - 98.8 (10.9)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A26D 
  "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A26D 
  "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "AMP PEAK  9(7Q34) MUTATED" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"AMP PEAK  9(7Q34) WILD-TYPE"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"AMP PEAK  9(7Q34) WILD-TYPE" "AMP PEAK  9(7Q34) WILD-TYPE" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "AMP PEAK  9(7Q34) MUTATED"   "AMP PEAK  9(7Q34) MUTATED" 
                 TCGA-GN-A26D 
  "AMP PEAK  9(7Q34) MUTATED" 
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(7Q34) MUTATED     21   41
  AMP PEAK  9(7Q34) WILD-TYPE   14   36
        clus
vv       AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE
  FEMALE                        21                          14
  MALE                          41                          36
                             vv
clus                          M0 M1 M1B M1C
  AMP PEAK  9(7Q34) MUTATED   53  1   1   1
  AMP PEAK  9(7Q34) WILD-TYPE 45  0   1   0
D9V4, multiclass
     clus
vv    AMP PEAK  9(7Q34) MUTATED AMP PEAK  9(7Q34) WILD-TYPE
  M0                         53                          45
  M1                          1                           0
  M1B                         1                           1
  M1C                         1                           0
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK  9(7Q34) MUTATED   30  1   2   7  0   3   4   1  7  2
  AMP PEAK  9(7Q34) WILD-TYPE 31  0   1   3  1   0   4   0  6  0
D9V5, multiclass
D9V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  9(7Q34) MUTATED             1       5        4        3        9
  AMP PEAK  9(7Q34) WILD-TYPE           0      10        3        8        4
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK  9(7Q34) MUTATED           4         1         2         2
  AMP PEAK  9(7Q34) WILD-TYPE         1         4         0         2
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  9(7Q34) MUTATED            3          7          9        2
  AMP PEAK  9(7Q34) WILD-TYPE          0          3          9        1
D9V7, multiclass

Clustering(10) Variable = Amp Peak 10(8q11.21) mutation analysis
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 10(8Q11.21) MUTATED   10 13
  AMP PEAK 10(8Q11.21) WILD-TYPE 17 19
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                            23                             36 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                            13                             19 
$`AMP PEAK 10(8Q11.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1HY 
       16.47        10.26        15.25        13.32        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29E 
       13.68        17.56         6.31         1.12        37.97        38.63 
TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.84         6.48         4.18        12.99        28.64        42.84 
TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26D 
       72.16        31.33        84.72        16.21        14.70 

$`AMP PEAK 10(8Q11.21) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       11.41         6.35        24.00         4.01         2.86        48.79 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A185 
       22.36         7.00        14.83        11.57        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        5.13        11.15         4.41         1.08         9.47        12.03 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        9.99         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A268 
       11.11        78.44         5.95        10.78         1.02        15.39 

  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                          1.12                           1.02 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE 
                         16.21                          11.23 
[1] "1.1 - 84.7 (16.2)" "1.0 - 98.8 (11.2)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 10(8Q11.21) WILD-TYPE"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 10(8Q11.21) WILD-TYPE" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 10(8Q11.21) MUTATED"   "AMP PEAK 10(8Q11.21) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 10(8Q11.21) MUTATED" "AMP PEAK 10(8Q11.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 10(8Q11.21) MUTATED" 
[1] "hr=" "1.5"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q11.21) MUTATED     13   28
  AMP PEAK 10(8Q11.21) WILD-TYPE   22   49
        clus
vv       AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  FEMALE                           13                             22
  MALE                             28                             49
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 10(8Q11.21) MUTATED   33  1   0   0
  AMP PEAK 10(8Q11.21) WILD-TYPE 65  0   2   1
D10V4, multiclass
     clus
vv    AMP PEAK 10(8Q11.21) MUTATED AMP PEAK 10(8Q11.21) WILD-TYPE
  M0                            33                             65
  M1                             1                              0
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 10(8Q11.21) MUTATED   21  1   1   5  0   0   2   0  4  1
  AMP PEAK 10(8Q11.21) WILD-TYPE 40  0   2   5  1   3   6   1  9  1
D10V5, multiclass
D10V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 10(8Q11.21) MUTATED             0       6        1        3        6
  AMP PEAK 10(8Q11.21) WILD-TYPE           1       9        6        8        7
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 10(8Q11.21) MUTATED           2         2         1         3
  AMP PEAK 10(8Q11.21) WILD-TYPE         3         3         1         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 10(8Q11.21) MUTATED            1          2          6        1
  AMP PEAK 10(8Q11.21) WILD-TYPE          2          8         12        2
D10V7, multiclass

Clustering(11) Variable = Amp Peak 11(8q24.21) mutation analysis
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(8Q24.21) MUTATED   11 15
  AMP PEAK 11(8Q24.21) WILD-TYPE 16 17
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            26                             33 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            15                             17 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HW 
       16.47        22.55        10.26        15.25        13.32        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 
       51.12        13.68         7.00        17.56         6.31         1.12 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
       37.97        38.63         4.41         1.08         8.84         9.99 
TCGA-EE-A29T TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A44A 
        6.48         4.18        12.99        28.64        42.84        72.16 
TCGA-GN-A267 TCGA-GN-A26D 
       16.21        14.70 

$`AMP PEAK 11(8Q24.21) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1IB 
        6.35        24.00         4.01         2.86        48.79        22.36 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D 
       14.83        11.57        12.20         4.27         5.13        11.15 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.47        12.03         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 
        8.94        11.11        78.44         5.95        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       31.33        84.72        15.39 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          1.08                           1.02 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         72.16                          98.76 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         14.19                          11.57 
[1] "1.1 - 72.2 (14.2)" "1.0 - 98.8 (11.6)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 11(8Q24.21) MUTATED"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 11(8Q24.21) WILD-TYPE"   "AMP PEAK 11(8Q24.21) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 11(8Q24.21) WILD-TYPE" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 11(8Q24.21) MUTATED" "AMP PEAK 11(8Q24.21) WILD-TYPE" 
                    TCGA-GN-A26D 
  "AMP PEAK 11(8Q24.21) MUTATED" 
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8Q24.21) MUTATED     16   34
  AMP PEAK 11(8Q24.21) WILD-TYPE   19   43
        clus
vv       AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  FEMALE                           16                             19
  MALE                             34                             43
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 11(8Q24.21) MUTATED   44  1   0   0
  AMP PEAK 11(8Q24.21) WILD-TYPE 54  0   2   1
D11V4, multiclass
     clus
vv    AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
  M0                            44                             54
  M1                             1                              0
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 11(8Q24.21) MUTATED   27  1   1   6  0   2   3   0  5  1
  AMP PEAK 11(8Q24.21) WILD-TYPE 34  0   2   4  1   1   5   1  8  1
D11V5, multiclass
D11V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 11(8Q24.21) MUTATED             0       7        2        5        7
  AMP PEAK 11(8Q24.21) WILD-TYPE           1       8        5        6        6
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 11(8Q24.21) MUTATED           3         2         1         3
  AMP PEAK 11(8Q24.21) WILD-TYPE         2         3         1         1
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 11(8Q24.21) MUTATED            1          5          7        1
  AMP PEAK 11(8Q24.21) WILD-TYPE          2          5         11        2
D11V7, multiclass

Clustering(12) Variable = Amp Peak 12(9p24.1) mutation analysis
D12V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 12(9P24.1) MUTATED    0  3
  AMP PEAK 12(9P24.1) WILD-TYPE 27 29
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            3                            56 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                            3                            29 
$`AMP PEAK 12(9P24.1) MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A3F3 TCGA-ER-A19M 
       22.55         7.00        28.64 

$`AMP PEAK 12(9P24.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       22.36        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
       11.11         4.18        12.99        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                         7.00                          1.02 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                        28.64                         98.76 
  AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE 
                       22.550                        12.595 
[1] "7.0 - 28.6 (22.6)" "1.0 - 98.8 (12.6)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK 12(9P24.1) WILD-TYPE"   "AMP PEAK 12(9P24.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK 12(9P24.1) WILD-TYPE"   "AMP PEAK 12(9P24.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "AMP PEAK 12(9P24.1) MUTATED" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"AMP PEAK 12(9P24.1) WILD-TYPE"   "AMP PEAK 12(9P24.1) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"AMP PEAK 12(9P24.1) WILD-TYPE" "AMP PEAK 12(9P24.1) WILD-TYPE" 
                   TCGA-GN-A26D 
"AMP PEAK 12(9P24.1) WILD-TYPE" 
[1] "hr=" "1.6"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(9P24.1) MUTATED      1    4
  AMP PEAK 12(9P24.1) WILD-TYPE   34   73
        clus
vv       AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  FEMALE                           1                            34
  MALE                             4                            73
                               vv
clus                            M0 M1 M1B M1C
  AMP PEAK 12(9P24.1) MUTATED    5  0   0   0
  AMP PEAK 12(9P24.1) WILD-TYPE 93  1   2   1
D12V4, multiclass
     clus
vv    AMP PEAK 12(9P24.1) MUTATED AMP PEAK 12(9P24.1) WILD-TYPE
  M0                            5                            93
  M1                            0                             1
  M1B                           0                             2
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 12(9P24.1) MUTATED    3  0   0   0  0   1   1   0  0  0
  AMP PEAK 12(9P24.1) WILD-TYPE 58  1   3  10  1   2   7   1 13  2
D12V5, multiclass
D12V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 12(9P24.1) MUTATED             0       2        0        1        0
  AMP PEAK 12(9P24.1) WILD-TYPE           1      13        7       10       13
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 12(9P24.1) MUTATED           0         0         0         0
  AMP PEAK 12(9P24.1) WILD-TYPE         5         5         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 12(9P24.1) MUTATED            0          2          0        0
  AMP PEAK 12(9P24.1) WILD-TYPE          3          8         18        3
D12V7, multiclass

Clustering(13) Variable = Amp Peak 13(11q13.3) mutation analysis
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(11Q13.3) MUTATED    4  7
  AMP PEAK 13(11Q13.3) WILD-TYPE 23 25
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                            11                             48 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                             7                             25 
$`AMP PEAK 13(11Q13.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A3F3 
       22.55        10.26        13.32        24.00         2.86         7.00 
TCGA-EE-A20F TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A268 TCGA-GN-A26D 
        5.13        28.64        42.84        15.39        14.70 

$`AMP PEAK 13(11Q13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        32.55        98.76        28.08         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW 
       11.41         6.35        15.25         4.01        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        13.68        22.36        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D 
        6.31         1.12        12.20         4.27        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 TCGA-FR-A3YN 
        8.94        11.11         4.18        12.99        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
       72.16        10.78         1.02        31.33        84.72        16.21 

  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                          2.86                           1.02 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                         42.84                          98.76 
  AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE 
                        14.700                         12.115 
[1] "2.9 - 42.8 (14.7)" "1.0 - 98.8 (12.1)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 13(11Q13.3) MUTATED"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 13(11Q13.3) MUTATED"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 13(11Q13.3) MUTATED"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 13(11Q13.3) MUTATED" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 13(11Q13.3) WILD-TYPE" "AMP PEAK 13(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 13(11Q13.3) WILD-TYPE"   "AMP PEAK 13(11Q13.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 13(11Q13.3) MUTATED" 
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q13.3) MUTATED      5   14
  AMP PEAK 13(11Q13.3) WILD-TYPE   30   63
        clus
vv       AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  FEMALE                            5                             30
  MALE                             14                             63
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 13(11Q13.3) MUTATED   17  0   0   0
  AMP PEAK 13(11Q13.3) WILD-TYPE 81  1   2   1
D13V4, multiclass
     clus
vv    AMP PEAK 13(11Q13.3) MUTATED AMP PEAK 13(11Q13.3) WILD-TYPE
  M0                            17                             81
  M1                             0                              1
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 13(11Q13.3) MUTATED   12  0   1   2  0   1   1   0  1  0
  AMP PEAK 13(11Q13.3) WILD-TYPE 49  1   2   8  1   2   7   1 12  2
D13V5, multiclass
D13V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 13(11Q13.3) MUTATED             0       4        0        2        2
  AMP PEAK 13(11Q13.3) WILD-TYPE           1      11        7        9       11
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 13(11Q13.3) MUTATED           1         2         1         1
  AMP PEAK 13(11Q13.3) WILD-TYPE         4         3         1         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 13(11Q13.3) MUTATED            1          3          1        0
  AMP PEAK 13(11Q13.3) WILD-TYPE          2          7         17        3
D13V7, multiclass

Clustering(14) Variable = Amp Peak 14(12q14.1) mutation analysis
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(12Q14.1) MUTATED    4 12
  AMP PEAK 14(12Q14.1) WILD-TYPE 23 20
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            16                             43 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                            12                             20 
$`AMP PEAK 14(12Q14.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-DA-A1HV 
       16.47        22.55        10.26        15.25        24.00        48.79 
TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2A6 TCGA-ER-A19M 
       35.80        17.56         6.31        11.15         8.94        28.64 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        16.21        15.39        14.70 

$`AMP PEAK 14(12Q14.1) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I2 
        6.35        13.32         4.01         2.86        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 
       22.36         7.00        14.83        11.57         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        4.27         5.13        37.97        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       11.31        25.28        23.90        11.11         4.18        12.99 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A265 
       84.72 

  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                          6.31                           1.02 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         48.79                          98.76 
  AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE 
                         16.34                          11.41 
[1] "6.3 - 48.8 (16.3)" "1.0 - 98.8 (11.4)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 14(12Q14.1) WILD-TYPE"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 14(12Q14.1) WILD-TYPE" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 14(12Q14.1) MUTATED" "AMP PEAK 14(12Q14.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 14(12Q14.1) MUTATED"   "AMP PEAK 14(12Q14.1) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 14(12Q14.1) MUTATED" 
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(12Q14.1) MUTATED      7   13
  AMP PEAK 14(12Q14.1) WILD-TYPE   28   64
        clus
vv       AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  FEMALE                            7                             28
  MALE                             13                             64
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 14(12Q14.1) MUTATED   18  0   0   0
  AMP PEAK 14(12Q14.1) WILD-TYPE 80  1   2   1
D14V4, multiclass
     clus
vv    AMP PEAK 14(12Q14.1) MUTATED AMP PEAK 14(12Q14.1) WILD-TYPE
  M0                            18                             80
  M1                             0                              1
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 14(12Q14.1) MUTATED   10  0   2   2  0   1   1   0  3  0
  AMP PEAK 14(12Q14.1) WILD-TYPE 51  1   1   8  1   2   7   1 10  2
D14V5, multiclass
D14V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 14(12Q14.1) MUTATED             0       2        1        2        1
  AMP PEAK 14(12Q14.1) WILD-TYPE           1      13        6        9       12
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 14(12Q14.1) MUTATED           0         3         1         0
  AMP PEAK 14(12Q14.1) WILD-TYPE         5         2         1         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 14(12Q14.1) MUTATED            2          3          4        0
  AMP PEAK 14(12Q14.1) WILD-TYPE          1          7         14        3
D14V7, multiclass

Clustering(15) Variable = Amp Peak 15(15q26.2) mutation analysis
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(15Q26.2) MUTATED    9 13
  AMP PEAK 15(15Q26.2) WILD-TYPE 18 19
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                            22                             37 
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                            13                             19 
$`AMP PEAK 15(15Q26.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A3Z3 
       32.55        22.55        21.14        11.41        13.32         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20F 
       48.79        35.80         7.00        17.56        12.20         5.13 
TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A1 TCGA-ER-A19M TCGA-FR-A44A 
       11.15         6.48         8.09        25.28        28.64        72.16 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        1.02        31.33        84.72        16.21 

$`AMP PEAK 15(15Q26.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2JK 
       16.47        98.76        28.08        10.26         8.38         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
       15.25        24.00         4.01        51.12        13.68        22.36 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29C 
       14.83        11.57         6.31         1.12         4.27        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       38.63         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        9.99        11.31        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-GN-A268 
       12.99        42.84        78.44         5.95        10.78        15.39 
TCGA-GN-A26D 
       14.70 

  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                          1.02                           1.08 
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE 
                        16.885                         11.570 
[1] "1.0 - 84.7 (16.9)" "1.1 - 98.8 (11.6)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 15(15Q26.2) WILD-TYPE" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 15(15Q26.2) WILD-TYPE"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 15(15Q26.2) MUTATED"   "AMP PEAK 15(15Q26.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 15(15Q26.2) MUTATED" "AMP PEAK 15(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 15(15Q26.2) WILD-TYPE" 
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.2) MUTATED     12   31
  AMP PEAK 15(15Q26.2) WILD-TYPE   23   46
        clus
vv       AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE
  FEMALE                           12                             23
  MALE                             31                             46
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 15(15Q26.2) MUTATED   37  0   1   0
  AMP PEAK 15(15Q26.2) WILD-TYPE 61  1   1   1
D15V4, multiclass
     clus
vv    AMP PEAK 15(15Q26.2) MUTATED AMP PEAK 15(15Q26.2) WILD-TYPE
  M0                            37                             61
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 15(15Q26.2) MUTATED   22  0   1   6  1   2   2   0  3  1
  AMP PEAK 15(15Q26.2) WILD-TYPE 39  1   2   4  0   1   6   1 10  1
D15V5, multiclass
D15V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 15(15Q26.2) MUTATED             1       7        3        3        7
  AMP PEAK 15(15Q26.2) WILD-TYPE           0       8        4        8        6
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 15(15Q26.2) MUTATED           1         0         0         2
  AMP PEAK 15(15Q26.2) WILD-TYPE         4         5         2         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 15(15Q26.2) MUTATED            2          5          5        0
  AMP PEAK 15(15Q26.2) WILD-TYPE          1          5         13        3
D15V7, multiclass

Clustering(16) Variable = Amp Peak 16(17q25.3) mutation analysis
D16V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 16(17Q25.3) MUTATED   12 13
  AMP PEAK 16(17Q25.3) WILD-TYPE 15 19
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                            25                             34 
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                            13                             19 
$`AMP PEAK 16(17Q25.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3CF TCGA-DA-A1HV 
       16.47        22.55        11.41        13.32        24.00        48.79 
TCGA-DA-A1HY TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F 
       51.12         7.00        17.56         1.12         4.27         5.13 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       11.15         4.41         1.08         9.47        12.03         8.84 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19N TCGA-FR-A3YN TCGA-GN-A265 TCGA-GN-A268 
        8.94        11.11        42.84         5.95        84.72        15.39 
TCGA-GN-A26D 
       14.70 

$`AMP PEAK 16(17Q25.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 
        6.35        15.25         4.01         2.86        35.80        13.68 
TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A29C 
       22.36        14.83        11.57         6.31        12.20        37.97 
TCGA-EE-A29E TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       38.63         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FR-A44A 
       23.90         4.18        12.99        28.64        78.44        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 
       10.78         1.02        31.33        16.21 

  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                          1.08                           1.02 
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE 
                        11.410                         14.255 
[1] "1.1 - 84.7 (11.4)" "1.0 - 98.8 (14.3)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 16(17Q25.3) MUTATED"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 16(17Q25.3) MUTATED" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 16(17Q25.3) WILD-TYPE" "AMP PEAK 16(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
"AMP PEAK 16(17Q25.3) WILD-TYPE"   "AMP PEAK 16(17Q25.3) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 16(17Q25.3) MUTATED" 
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17Q25.3) MUTATED     13   31
  AMP PEAK 16(17Q25.3) WILD-TYPE   22   46
        clus
vv       AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE
  FEMALE                           13                             22
  MALE                             31                             46
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 16(17Q25.3) MUTATED   39  0   1   0
  AMP PEAK 16(17Q25.3) WILD-TYPE 59  1   1   1
D16V4, multiclass
     clus
vv    AMP PEAK 16(17Q25.3) MUTATED AMP PEAK 16(17Q25.3) WILD-TYPE
  M0                            39                             59
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 16(17Q25.3) MUTATED   25  0   1   4  0   2   2   0  7  0
  AMP PEAK 16(17Q25.3) WILD-TYPE 36  1   2   6  1   1   6   1  6  2
D16V5, multiclass
D16V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 16(17Q25.3) MUTATED             0       4        4        3        6
  AMP PEAK 16(17Q25.3) WILD-TYPE           1      11        3        8        7
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 16(17Q25.3) MUTATED           1         3         2         1
  AMP PEAK 16(17Q25.3) WILD-TYPE         4         2         0         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 16(17Q25.3) MUTATED            1          3          9        0
  AMP PEAK 16(17Q25.3) WILD-TYPE          2          7          9        3
D16V7, multiclass

Clustering(17) Variable = Amp Peak 17(19p13.2) mutation analysis
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(19P13.2) MUTATED    5  4
  AMP PEAK 17(19P13.2) WILD-TYPE 22 28
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                             9                             50 
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                             4                             28 
$`AMP PEAK 17(19P13.2) MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R 
       32.55        17.56        38.63         1.08        12.03         8.84 
TCGA-ER-A19J TCGA-FR-A3YN TCGA-GN-A267 
        4.18         5.95        16.21 

$`AMP PEAK 17(19P13.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        4.01         2.86        48.79        35.80        51.12        13.68 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       22.36         7.00        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
       12.20         4.27         5.13        37.97        11.15         4.41 
TCGA-EE-A29N TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.47         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       23.90         8.94        11.11        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
       78.44        72.16        10.78         1.02        31.33        84.72 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                          1.08                           1.02 
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                         38.63                          98.76 
  AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE 
                        12.030                         13.155 
[1] "1.1 - 38.6 (12.0)" "1.0 - 98.8 (13.2)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 17(19P13.2) WILD-TYPE"   "AMP PEAK 17(19P13.2) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"AMP PEAK 17(19P13.2) WILD-TYPE" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 17(19P13.2) MUTATED" "AMP PEAK 17(19P13.2) WILD-TYPE" 
                    TCGA-GN-A26D 
"AMP PEAK 17(19P13.2) WILD-TYPE" 
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(19P13.2) MUTATED      4   15
  AMP PEAK 17(19P13.2) WILD-TYPE   31   62
        clus
vv       AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE
  FEMALE                            4                             31
  MALE                             15                             62
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 17(19P13.2) MUTATED   18  1   0   0
  AMP PEAK 17(19P13.2) WILD-TYPE 80  0   2   1
D17V4, multiclass
     clus
vv    AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE
  M0                            18                             80
  M1                             1                              0
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 17(19P13.2) MUTATED   12  0   1   3  0   0   0   0  3  0
  AMP PEAK 17(19P13.2) WILD-TYPE 49  1   2   7  1   3   8   1 10  2
D17V5, multiclass
D17V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 17(19P13.2) MUTATED             1       6        0        1        2
  AMP PEAK 17(19P13.2) WILD-TYPE           0       9        7       10       11
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 17(19P13.2) MUTATED           1         0         1         0
  AMP PEAK 17(19P13.2) WILD-TYPE         4         5         1         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 17(19P13.2) MUTATED            1          1          4        1
  AMP PEAK 17(19P13.2) WILD-TYPE          2          9         14        2
D17V7, multiclass

Clustering(18) Variable = Amp Peak 18(22q13.2) mutation analysis
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(22Q13.2) MUTATED   12 13
  AMP PEAK 18(22Q13.2) WILD-TYPE 15 19
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                            25                             34 
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                            13                             19 
$`AMP PEAK 18(22Q13.2) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW 
       16.47        22.55        13.32         4.01        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A29L TCGA-EE-A29N 
       51.12        22.36        17.56         6.31         1.08         9.47 
TCGA-EE-A29R TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19L TCGA-ER-A19M 
        8.84         8.09        23.90         8.94        12.99        28.64 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        5.95        72.16        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

$`AMP PEAK 18(22Q13.2) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1I2 
       11.41         6.35        15.25        24.00         2.86        13.68 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
        7.00        14.83        11.57         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
        5.13        37.97        11.15        38.63         4.41        12.03 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-ER-A19F TCGA-ER-A19J 
        9.99         6.48        11.31        25.28        11.11         4.18 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44        10.78         1.02 

  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                          1.08                           1.02 
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE 
                         16.21                          11.36 
[1] "1.1 - 84.7 (16.2)" "1.0 - 98.8 (11.4)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "AMP PEAK 18(22Q13.2) MUTATED" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"AMP PEAK 18(22Q13.2) WILD-TYPE"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"AMP PEAK 18(22Q13.2) WILD-TYPE" "AMP PEAK 18(22Q13.2) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "AMP PEAK 18(22Q13.2) MUTATED"   "AMP PEAK 18(22Q13.2) MUTATED" 
                    TCGA-GN-A26D 
  "AMP PEAK 18(22Q13.2) MUTATED" 
[1] "hr=" "1.4"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(22Q13.2) MUTATED     15   33
  AMP PEAK 18(22Q13.2) WILD-TYPE   20   44
        clus
vv       AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE
  FEMALE                           15                             20
  MALE                             33                             44
                                vv
clus                             M0 M1 M1B M1C
  AMP PEAK 18(22Q13.2) MUTATED   39  0   1   1
  AMP PEAK 18(22Q13.2) WILD-TYPE 59  1   1   0
D18V4, multiclass
     clus
vv    AMP PEAK 18(22Q13.2) MUTATED AMP PEAK 18(22Q13.2) WILD-TYPE
  M0                            39                             59
  M1                             0                              1
  M1B                            1                              1
  M1C                            1                              0
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  AMP PEAK 18(22Q13.2) MUTATED   21  0   3   5  0   2   3   1  6  1
  AMP PEAK 18(22Q13.2) WILD-TYPE 40  1   0   5  1   1   5   0  7  1
D18V5, multiclass
D18V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 18(22Q13.2) MUTATED             0       5        3        3        5
  AMP PEAK 18(22Q13.2) WILD-TYPE           1      10        4        8        8
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  AMP PEAK 18(22Q13.2) MUTATED           1         2         1         1
  AMP PEAK 18(22Q13.2) WILD-TYPE         4         3         1         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 18(22Q13.2) MUTATED            3          5          9        1
  AMP PEAK 18(22Q13.2) WILD-TYPE          0          5          9        2
D18V7, multiclass

Clustering(19) Variable = Del Peak  1(1p36.31) mutation analysis
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    5  6
  DEL PEAK  1(1P36.31) WILD-TYPE 22 26
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            11                             48 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             6                             26 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1I2 TCGA-DA-A3F5 
       16.47         6.35        15.25        13.32        13.68        17.56 
TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29R TCGA-GN-A26D 
       14.83         5.13        11.15         8.84        14.70 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       21.14        11.41        24.00         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z 
       35.80        51.12        22.36         7.00        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        1.12        12.20         4.27        37.97        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        1.08         9.47        12.03         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          5.13                           1.02 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         17.56                          98.76 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        13.680                         12.115 
[1] "5.1 - 17.6 (13.7)" "1.0 - 98.8 (12.1)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"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-A26D 
  "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"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-A26D 
  "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"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-A26D 
  "DEL PEAK  1(1P36.31) MUTATED" 
[1] "hr=" "1.4"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     10   17
  DEL PEAK  1(1P36.31) WILD-TYPE   25   60
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           10                             25
  MALE                             17                             60
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK  1(1P36.31) MUTATED   23  0   0   0
  DEL PEAK  1(1P36.31) WILD-TYPE 75  1   2   1
D19V4, multiclass
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                            23                             75
  M1                             0                              1
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  1(1P36.31) MUTATED   12  0   1   4  0   0   4   0  2  1
  DEL PEAK  1(1P36.31) WILD-TYPE 49  1   2   6  1   3   4   1 11  1
D19V5, multiclass
D19V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  1(1P36.31) MUTATED             0       3        1        2        5
  DEL PEAK  1(1P36.31) WILD-TYPE           1      12        6        9        8
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  1(1P36.31) MUTATED           0         0         1         2
  DEL PEAK  1(1P36.31) WILD-TYPE         5         5         1         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.31) MUTATED            0          2          7        0
  DEL PEAK  1(1P36.31) WILD-TYPE          3          8         11        3
D19V7, multiclass

Clustering(20) Variable = Del Peak  2(1p21.3) mutation analysis
D20V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P21.3) MUTATED    7 10
  DEL PEAK  2(1P21.3) WILD-TYPE 20 22
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           17                            42 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                           10                            22 
$`DEL PEAK  2(1P21.3) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE 
       28.08        22.55        10.26        11.41        15.25        13.32 
TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A29C TCGA-EE-A29D 
        2.86        13.68        17.56        14.83        37.97        11.15 
TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19L TCGA-ER-A19M TCGA-GN-A26D 
        8.84         6.48        12.99        28.64        14.70 

$`DEL PEAK  2(1P21.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       16.47        32.55        98.76         8.38        21.14         6.35 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1IB 
       24.00         4.01        48.79        35.80        51.12        22.36 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
        7.00        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        5.13        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        9.99         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       11.11         4.18        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       10.78         1.02        31.33        84.72        16.21        15.39 

  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                         2.86                          1.02 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                        37.97                         98.76 
  DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE 
                        13.68                         11.80 
[1] "2.9 - 38.0 (13.7)" "1.0 - 98.8 (11.8)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  2(1P21.3) WILD-TYPE"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  2(1P21.3) MUTATED" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK  2(1P21.3) MUTATED"   "DEL PEAK  2(1P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  2(1P21.3) WILD-TYPE" "DEL PEAK  2(1P21.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  2(1P21.3) MUTATED" 
[1] "hr=" "1.2"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P21.3) MUTATED      9   21
  DEL PEAK  2(1P21.3) WILD-TYPE   26   56
        clus
vv       DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  FEMALE                           9                            26
  MALE                            21                            56
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  2(1P21.3) MUTATED   25  0   1   0
  DEL PEAK  2(1P21.3) WILD-TYPE 73  1   1   1
D20V4, multiclass
     clus
vv    DEL PEAK  2(1P21.3) MUTATED DEL PEAK  2(1P21.3) WILD-TYPE
  M0                           25                            73
  M1                            0                             1
  M1B                           1                             1
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  2(1P21.3) MUTATED   13  0   1   6  0   1   3   0  2  1
  DEL PEAK  2(1P21.3) WILD-TYPE 48  1   2   4  1   2   5   1 11  1
D20V5, multiclass
D20V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  2(1P21.3) MUTATED             0       3        0        3        4
  DEL PEAK  2(1P21.3) WILD-TYPE           1      12        7        8        9
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  2(1P21.3) MUTATED           0         2         1         2
  DEL PEAK  2(1P21.3) WILD-TYPE         5         3         1         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  2(1P21.3) MUTATED            0          4          6        1
  DEL PEAK  2(1P21.3) WILD-TYPE          3          6         12        2
D20V7, multiclass

Clustering(21) Variable = Del Peak  3(2q37.3) mutation analysis
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q37.3) MUTATED    6  6
  DEL PEAK  3(2Q37.3) WILD-TYPE 21 26
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           12                            47 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            6                            26 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       11.41         6.35        15.25         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29P TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
       38.63        12.03        72.16        31.33        16.21        14.70 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        8.38        21.14        13.32        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 
       48.79        35.80        51.12        13.68        22.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
        4.27         4.41         1.08         9.47         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 
        5.95        10.78         1.02        84.72        15.39 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         5.13                          1.02 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        72.16                         98.76 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       14.975                        12.200 
[1] "5.1 - 72.2 (15.0)" "1.0 - 98.8 (12.2)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A26D 
  "DEL PEAK  3(2Q37.3) MUTATED" 
[1] "hr=" "1.4"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      7   14
  DEL PEAK  3(2Q37.3) WILD-TYPE   28   63
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                           7                            28
  MALE                            14                            63
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  3(2Q37.3) MUTATED   17  0   1   0
  DEL PEAK  3(2Q37.3) WILD-TYPE 81  1   1   1
D21V4, multiclass
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  M0                           17                            81
  M1                            0                             1
  M1B                           1                             1
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  3(2Q37.3) MUTATED   13  0   1   3  0   0   1   0  1  0
  DEL PEAK  3(2Q37.3) WILD-TYPE 48  1   2   7  1   3   7   1 12  2
D21V5, multiclass
D21V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  3(2Q37.3) MUTATED             0       1        0        3        6
  DEL PEAK  3(2Q37.3) WILD-TYPE           1      14        7        8        7
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  3(2Q37.3) MUTATED           0         1         2         0
  DEL PEAK  3(2Q37.3) WILD-TYPE         5         4         0         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED            1          1          3        0
  DEL PEAK  3(2Q37.3) WILD-TYPE          2          9         15        3
D21V7, multiclass

Clustering(22) Variable = Del Peak  4(3p24.3) mutation analysis
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P24.3) MUTATED    5  5
  DEL PEAK  4(3P24.3) WILD-TYPE 22 27
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                           10                            49 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                            5                            27 
$`DEL PEAK  4(3P24.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        98.76        15.25        48.79        35.80        13.68 
TCGA-EE-A20F TCGA-EE-A29P TCGA-FR-A44A TCGA-GN-A267 
        5.13        12.03        72.16        16.21 

$`DEL PEAK  4(3P24.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        28.08        22.55        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       11.41         6.35        13.32        24.00         4.01         2.86 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        22.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D 
        6.31         1.12        12.20         4.27        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       38.63         4.41         1.08         9.47         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
        5.95        10.78         1.02        31.33        84.72        15.39 
TCGA-GN-A26D 
       14.70 

  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                         5.13                          1.02 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                        98.76                         84.72 
  DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE 
                        24.38                         11.41 
[1] "5.1 - 98.8 (24.4)" "1.0 - 84.7 (11.4)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  4(3P24.3) WILD-TYPE"   "DEL PEAK  4(3P24.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  4(3P24.3) WILD-TYPE" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  4(3P24.3) MUTATED" "DEL PEAK  4(3P24.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  4(3P24.3) WILD-TYPE" 
[1] "hr=" "1.9"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P24.3) MUTATED      8    9
  DEL PEAK  4(3P24.3) WILD-TYPE   27   68
        clus
vv       DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  FEMALE                           8                            27
  MALE                             9                            68
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  4(3P24.3) MUTATED   16  0   0   0
  DEL PEAK  4(3P24.3) WILD-TYPE 82  1   2   1
D22V4, multiclass
     clus
vv    DEL PEAK  4(3P24.3) MUTATED DEL PEAK  4(3P24.3) WILD-TYPE
  M0                           16                            82
  M1                            0                             1
  M1B                           0                             2
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  4(3P24.3) MUTATED   10  1   1   1  0   0   3   0  0  0
  DEL PEAK  4(3P24.3) WILD-TYPE 51  0   2   9  1   3   5   1 13  2
D22V5, multiclass
D22V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  4(3P24.3) MUTATED             1       1        0        2        5
  DEL PEAK  4(3P24.3) WILD-TYPE           0      14        7        9        8
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  4(3P24.3) MUTATED           0         0         1         2
  DEL PEAK  4(3P24.3) WILD-TYPE         5         5         1         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  4(3P24.3) MUTATED            1          2          1        0
  DEL PEAK  4(3P24.3) WILD-TYPE          2          8         17        3
D22V7, multiclass

Clustering(23) Variable = Del Peak  5(4q34.3) mutation analysis
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(4Q34.3) MUTATED    6  6
  DEL PEAK  5(4Q34.3) WILD-TYPE 21 26
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                           12                            47 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                            6                            26 
$`DEL PEAK  5(4Q34.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A3F5 
       16.47        28.08        11.41        35.80        51.12        17.56 
TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A6 
       14.83         1.12        37.97         6.48         8.09         8.94 

$`DEL PEAK  5(4Q34.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        22.55        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 
        6.35        15.25        13.32        24.00         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z 
       48.79        13.68        22.36         7.00        11.57         6.31 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27         5.13        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 
        1.08         9.47        12.03         8.84         9.99        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       25.28        23.90        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       42.84        78.44         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                         1.12                          1.02 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        51.12                         98.76 
  DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE 
                        15.65                         12.20 
[1] "1.1 - 51.1 (15.6)" "1.0 - 98.8 (12.2)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
  "DEL PEAK  5(4Q34.3) MUTATED" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  5(4Q34.3) MUTATED"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK  5(4Q34.3) WILD-TYPE"   "DEL PEAK  5(4Q34.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  5(4Q34.3) WILD-TYPE" "DEL PEAK  5(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  5(4Q34.3) WILD-TYPE" 
[1] "hr=" "1.3"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q34.3) MUTATED     10   13
  DEL PEAK  5(4Q34.3) WILD-TYPE   25   64
        clus
vv       DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  FEMALE                          10                            25
  MALE                            13                            64
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  5(4Q34.3) MUTATED   21  0   2   0
  DEL PEAK  5(4Q34.3) WILD-TYPE 77  1   0   1
D23V4, multiclass
     clus
vv    DEL PEAK  5(4Q34.3) MUTATED DEL PEAK  5(4Q34.3) WILD-TYPE
  M0                           21                            77
  M1                            0                             1
  M1B                           2                             0
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  5(4Q34.3) MUTATED   12  0   0   2  0   1   2   0  5  1
  DEL PEAK  5(4Q34.3) WILD-TYPE 49  1   3   8  1   2   6   1  8  1
D23V5, multiclass
D23V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  5(4Q34.3) MUTATED             0       5        3        3        1
  DEL PEAK  5(4Q34.3) WILD-TYPE           1      10        4        8       12
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  5(4Q34.3) MUTATED           0         0         0         0
  DEL PEAK  5(4Q34.3) WILD-TYPE         5         5         2         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  5(4Q34.3) MUTATED            1          2          5        1
  DEL PEAK  5(4Q34.3) WILD-TYPE          2          8         13        2
D23V7, multiclass

Clustering(24) Variable = Del Peak  6(5q31.3) mutation analysis
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(5Q31.3) MUTATED   10 14
  DEL PEAK  6(5Q31.3) WILD-TYPE 17 18
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                           24                            35 
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                           14                            18 
$`DEL PEAK  6(5Q31.3) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
       28.08        22.55        11.41         6.35        15.25        24.00 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A3F5 TCGA-EE-A17X 
        4.01        48.79        35.80        51.12        17.56        11.57 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29S 
        6.31         4.27        37.97        38.63        12.03         9.99 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-FR-A44A TCGA-GN-A267 TCGA-GN-A268 
        8.09        11.31        23.90        72.16        16.21        15.39 

$`DEL PEAK  6(5Q31.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        32.55        98.76        10.26         8.38        21.14 
TCGA-D3-A3CE TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 
       13.32         2.86        13.68        22.36         7.00        14.83 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        1.12        12.20         5.13        11.15         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F 
        9.47         8.84         6.48        25.28         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A26D 
       10.78         1.02        31.33        84.72        14.70 

  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                         4.01                          1.02 
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                        72.16                         98.76 
  DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE 
                        15.80                         11.15 
[1] "4.0 - 72.2 (15.8)" "1.0 - 98.8 (11.2)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  6(5Q31.3) MUTATED" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  6(5Q31.3) WILD-TYPE"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A264                    TCGA-GN-A265 
"DEL PEAK  6(5Q31.3) WILD-TYPE" "DEL PEAK  6(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  6(5Q31.3) MUTATED"   "DEL PEAK  6(5Q31.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  6(5Q31.3) WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(5Q31.3) MUTATED     15   30
  DEL PEAK  6(5Q31.3) WILD-TYPE   20   47
        clus
vv       DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE
  FEMALE                          15                            20
  MALE                            30                            47
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  6(5Q31.3) MUTATED   41  0   2   0
  DEL PEAK  6(5Q31.3) WILD-TYPE 57  1   0   1
D24V4, multiclass
     clus
vv    DEL PEAK  6(5Q31.3) MUTATED DEL PEAK  6(5Q31.3) WILD-TYPE
  M0                           41                            57
  M1                            0                             1
  M1B                           2                             0
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  6(5Q31.3) MUTATED   24  0   3   4  0   2   2   0  7  1
  DEL PEAK  6(5Q31.3) WILD-TYPE 37  1   0   6  1   1   6   1  6  1
D24V5, multiclass
D24V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  6(5Q31.3) MUTATED             0       6        4        3        4
  DEL PEAK  6(5Q31.3) WILD-TYPE           1       9        3        8        9
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  6(5Q31.3) MUTATED           3         3         1         0
  DEL PEAK  6(5Q31.3) WILD-TYPE         2         2         1         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  6(5Q31.3) MUTATED            3          6          7        1
  DEL PEAK  6(5Q31.3) WILD-TYPE          0          4         11        2
D24V7, multiclass

Clustering(25) Variable = Del Peak  7(6q25.3) mutation analysis
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(6Q25.3) MUTATED   16 20
  DEL PEAK  7(6Q25.3) WILD-TYPE 11 12
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                           36                            23 
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                           20                            12 
$`DEL PEAK  7(6Q25.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3C6 
       16.47        32.55        22.55        10.26        11.41        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A3F3 
       13.32        24.00         2.86        48.79        51.12         7.00 
TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
       17.56         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       11.15         4.41         1.08         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        8.09        25.28        23.90         8.94        11.11         4.18 
TCGA-ER-A19N TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       42.84        10.78         1.02        31.33        16.21        15.39 

$`DEL PEAK  7(6Q25.3) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D9-A3Z1 
       98.76        28.08         8.38        21.14         6.35         4.01 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       35.80        13.68        22.36        14.83        11.57         6.31 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-ER-A19L TCGA-ER-A19M 
       38.63         9.47        12.03        11.31        12.99        28.64 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A265 TCGA-GN-A26D 
       78.44         5.95        72.16        84.72        14.70 

  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                         1.02                          4.01 
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                        51.12                         98.76 
  DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE 
                        11.28                         14.70 
[1] "1.0 - 51.1 (11.3)" "4.0 - 98.8 (14.7)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  7(6Q25.3) WILD-TYPE"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  7(6Q25.3) WILD-TYPE" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  7(6Q25.3) MUTATED" "DEL PEAK  7(6Q25.3) WILD-TYPE" 
                   TCGA-GN-A267                    TCGA-GN-A268 
  "DEL PEAK  7(6Q25.3) MUTATED"   "DEL PEAK  7(6Q25.3) MUTATED" 
                   TCGA-GN-A26D 
"DEL PEAK  7(6Q25.3) WILD-TYPE" 
[1] "hr=" "1.4"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(6Q25.3) MUTATED     22   45
  DEL PEAK  7(6Q25.3) WILD-TYPE   13   32
        clus
vv       DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE
  FEMALE                          22                            13
  MALE                            45                            32
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  7(6Q25.3) MUTATED   58  1   1   1
  DEL PEAK  7(6Q25.3) WILD-TYPE 40  0   1   0
D25V4, multiclass
     clus
vv    DEL PEAK  7(6Q25.3) MUTATED DEL PEAK  7(6Q25.3) WILD-TYPE
  M0                           58                            40
  M1                            1                             0
  M1B                           1                             1
  M1C                           1                             0
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  7(6Q25.3) MUTATED   33  0   3   7  1   2   3   1  9  2
  DEL PEAK  7(6Q25.3) WILD-TYPE 28  1   0   3  0   1   5   0  4  0
D25V5, multiclass
D25V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  7(6Q25.3) MUTATED             1       7        3        7        9
  DEL PEAK  7(6Q25.3) WILD-TYPE           0       8        4        4        4
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  7(6Q25.3) MUTATED           3         2         0         2
  DEL PEAK  7(6Q25.3) WILD-TYPE         2         3         2         2
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  7(6Q25.3) MUTATED            2          7         11        2
  DEL PEAK  7(6Q25.3) WILD-TYPE          1          3          7        1
D25V7, multiclass

Clustering(26) Variable = Del Peak  8(6q26) mutation analysis
D26V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  8(6Q26) MUTATED   14 20
  DEL PEAK  8(6Q26) WILD-TYPE 13 12
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         34                          25 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         20                          12 
$`DEL PEAK  8(6Q26) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3C6 
       16.47        32.55        22.55        10.26        11.41        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A3F3 
       13.32        24.00         2.86        48.79        51.12         7.00 
TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29D 
       17.56         1.12        12.20         4.27        37.97        11.15 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        4.41         1.08         8.84         9.99         6.48         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N 
       25.28        23.90         8.94        11.11         4.18        42.84 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
        1.02        31.33        16.21        15.39 

$`DEL PEAK  8(6Q26) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D9-A3Z1 
       98.76        28.08         8.38        21.14         6.35         4.01 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       35.80        13.68        22.36        14.83        11.57         6.31 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A0 TCGA-ER-A19L 
        5.13        38.63         9.47        12.03        11.31        12.99 
TCGA-ER-A19M TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-GN-A265 
       28.64        78.44         5.95        72.16        10.78        84.72 
TCGA-GN-A26D 
       14.70 

  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                       1.02                        4.01 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                      51.12                       98.76 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                     11.805                      13.680 
[1] "1.0 - 51.1 (11.8)" "4.0 - 98.8 (13.7)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A26D 
"DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A26D 
"DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
"DEL PEAK  8(6Q26) WILD-TYPE" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
"DEL PEAK  8(6Q26) WILD-TYPE"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK  8(6Q26) MUTATED" "DEL PEAK  8(6Q26) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
  "DEL PEAK  8(6Q26) MUTATED"   "DEL PEAK  8(6Q26) MUTATED" 
                 TCGA-GN-A26D 
"DEL PEAK  8(6Q26) WILD-TYPE" 
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(6Q26) MUTATED     22   41
  DEL PEAK  8(6Q26) WILD-TYPE   13   36
        clus
vv       DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE
  FEMALE                        22                          13
  MALE                          41                          36
                             vv
clus                          M0 M1 M1B M1C
  DEL PEAK  8(6Q26) MUTATED   54  1   1   1
  DEL PEAK  8(6Q26) WILD-TYPE 44  0   1   0
D26V4, multiclass
     clus
vv    DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE
  M0                         54                          44
  M1                          1                           0
  M1B                         1                           1
  M1C                         1                           0
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  8(6Q26) MUTATED   30  0   3   7  1   2   3   1  8  2
  DEL PEAK  8(6Q26) WILD-TYPE 31  1   0   3  0   1   5   0  5  0
D26V5, multiclass
D26V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  8(6Q26) MUTATED             1       7        3        7        6
  DEL PEAK  8(6Q26) WILD-TYPE           0       8        4        4        7
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  8(6Q26) MUTATED           3         2         0         2
  DEL PEAK  8(6Q26) WILD-TYPE         2         3         2         2
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  8(6Q26) MUTATED            2          7         10        2
  DEL PEAK  8(6Q26) WILD-TYPE          1          3          8        1
D26V7, multiclass

Clustering(27) Variable = Del Peak  9(8p23.3) mutation analysis
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(8P23.3) MUTATED    5 10
  DEL PEAK  9(8P23.3) WILD-TYPE 22 22
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                           15                            44 
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                           10                            22 
$`DEL PEAK  9(8P23.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-DA-A3F3 
       16.47        22.55        10.26        11.41        15.25         7.00 
TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A2A2 TCGA-ER-A19J 
       12.20        37.97         4.41         1.08        23.90         4.18 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 
        1.02        31.33        84.72 

$`DEL PEAK  9(8P23.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       32.55        98.76        28.08         8.38        21.14         6.35 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       13.32        24.00         4.01         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       51.12        13.68        22.36        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E 
        6.31         1.12         4.27         5.13        11.15        38.63 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M 
       11.31        25.28         8.94        11.11        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-GN-A267 
       42.84        78.44         5.95        72.16        10.78        16.21 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                         1.02                          1.12 
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                        84.72                         98.76 
  DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE 
                       12.200                        13.155 
[1] "1.0 - 84.7 (12.2)" "1.1 - 98.8 (13.2)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A185 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
  "DEL PEAK  9(8P23.3) MUTATED" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
"DEL PEAK  9(8P23.3) WILD-TYPE"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK  9(8P23.3) MUTATED"   "DEL PEAK  9(8P23.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK  9(8P23.3) WILD-TYPE" "DEL PEAK  9(8P23.3) WILD-TYPE" 
                   TCGA-GN-A26D 
"DEL PEAK  9(8P23.3) WILD-TYPE" 
[1] "hr=" "1.4"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(8P23.3) MUTATED      7   22
  DEL PEAK  9(8P23.3) WILD-TYPE   28   55
        clus
vv       DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE
  FEMALE                           7                            28
  MALE                            22                            55
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK  9(8P23.3) MUTATED   23  1   1   0
  DEL PEAK  9(8P23.3) WILD-TYPE 75  0   1   1
D27V4, multiclass
     clus
vv    DEL PEAK  9(8P23.3) MUTATED DEL PEAK  9(8P23.3) WILD-TYPE
  M0                           23                            75
  M1                            1                             0
  M1B                           1                             1
  M1C                           0                             1
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK  9(8P23.3) MUTATED   15  0   0   2  1   2   1   0  4  0
  DEL PEAK  9(8P23.3) WILD-TYPE 46  1   3   8  0   1   7   1  9  2
D27V5, multiclass
D27V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  9(8P23.3) MUTATED             0       6        2        3        2
  DEL PEAK  9(8P23.3) WILD-TYPE           1       9        5        8       11
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK  9(8P23.3) MUTATED           0         2         0         1
  DEL PEAK  9(8P23.3) WILD-TYPE         5         3         2         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  9(8P23.3) MUTATED            0          3          3        1
  DEL PEAK  9(8P23.3) WILD-TYPE          3          7         15        2
D27V7, multiclass

Clustering(28) Variable = Del Peak 10(9p23) mutation analysis
D28V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 10(9P23) MUTATED   17 23
  DEL PEAK 10(9P23) WILD-TYPE 10  9
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                         40                          19 
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                         23                           9 
$`DEL PEAK 10(9P23) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 
       16.47        32.55        28.08        10.26         6.35        15.25 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       24.00         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F 
       13.68         7.00        11.57         1.12         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19F 
        9.99         6.48         8.09        11.31         8.94        11.11 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       12.99        28.64        42.84         5.95        72.16        10.78 
TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
        1.02        31.33        15.39        14.70 

$`DEL PEAK 10(9P23) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
       98.76        22.55         8.38        21.14        11.41        13.32 
TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A29H 
       22.36        17.56        14.83         6.31        12.20         4.41 
TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19J TCGA-ER-A1A1 TCGA-GN-A265 
        8.84        25.28        23.90         4.18        78.44        84.72 
TCGA-GN-A267 
       16.21 

  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                       1.02                        4.18 
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                      72.16                       98.76 
  DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE 
                      11.44                       16.21 
[1] "1.0 - 72.2 (11.4)" "4.2 - 98.8 (16.2)"
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK 10(9P23) WILD-TYPE" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A26D 
  "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK 10(9P23) WILD-TYPE" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A26D 
  "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q1                  TCGA-D3-A1Q5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q8 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A1Q9                  TCGA-D3-A2J6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A2J8                  TCGA-D3-A2J9 
"DEL PEAK 10(9P23) WILD-TYPE" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A2JD                  TCGA-D3-A2JK 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D3-A3C6                  TCGA-D3-A3CE 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-D9-A3Z1 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-D9-A3Z3                  TCGA-DA-A1HV 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-DA-A1I2                  TCGA-DA-A1IB 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F3                  TCGA-DA-A3F5 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-DA-A3F8                  TCGA-EE-A17X 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A17Z                  TCGA-EE-A181 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A185 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A29C 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29D                  TCGA-EE-A29E 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29H                  TCGA-EE-A29L 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29N                  TCGA-EE-A29P 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29R                  TCGA-EE-A29S 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A29X 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-EE-A2A0                  TCGA-EE-A2A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2A6 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19F                  TCGA-ER-A19J 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-ER-A19L                  TCGA-ER-A19M 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-ER-A19N                  TCGA-ER-A1A1 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-FR-A3YN                  TCGA-FR-A44A 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-FS-A4F9                  TCGA-FW-A3R5 
  "DEL PEAK 10(9P23) MUTATED"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A264                  TCGA-GN-A265 
  "DEL PEAK 10(9P23) MUTATED" "DEL PEAK 10(9P23) WILD-TYPE" 
                 TCGA-GN-A267                  TCGA-GN-A268 
"DEL PEAK 10(9P23) WILD-TYPE"   "DEL PEAK 10(9P23) MUTATED" 
                 TCGA-GN-A26D 
  "DEL PEAK 10(9P23) MUTATED" 
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(9P23) MUTATED     26   49
  DEL PEAK 10(9P23) WILD-TYPE    9   28
        clus
vv       DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE
  FEMALE                        26                           9
  MALE                          49                          28
                             vv
clus                          M0 M1 M1B M1C
  DEL PEAK 10(9P23) MUTATED   65  0   1   1
  DEL PEAK 10(9P23) WILD-TYPE 33  1   1   0
D28V4, multiclass
     clus
vv    DEL PEAK 10(9P23) MUTATED DEL PEAK 10(9P23) WILD-TYPE
  M0                         65                          33
  M1                          0                           1
  M1B                         1                           1
  M1C                         1                           0
                             vv
clus                          N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 10(9P23) MUTATED   42  1   2   6  1   0   5   1  8  2
  DEL PEAK 10(9P23) WILD-TYPE 19  0   1   4  0   3   3   0  5  0
D28V5, multiclass
D28V6, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 10(9P23) MUTATED             1       7        5        7       10
  DEL PEAK 10(9P23) WILD-TYPE           0       8        2        4        3
                             vv
clus                          STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 10(9P23) MUTATED           4         4         2         3
  DEL PEAK 10(9P23) WILD-TYPE         1         1         0         1
                             vv
clus                          STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 10(9P23) MUTATED            1          7         11        2
  DEL PEAK 10(9P23) WILD-TYPE          2          3          7        1
D28V7, multiclass

Clustering(29) Variable = Del Peak 11(9p21.3) mutation analysis
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(9P21.3) MUTATED   21 25
  DEL PEAK 11(9P21.3) WILD-TYPE  6  7
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           46                            13 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                           25                             7 
$`DEL PEAK 11(9P21.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JK TCGA-D3-A3C6 
       16.47        32.55        28.08        10.26         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       13.32        24.00         4.01         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 
       51.12        13.68         7.00        17.56        11.57         1.12 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.47        12.03         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        8.09        11.31         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 
       28.64        42.84         5.95        72.16        10.78         1.02 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        15.39        14.70 

$`DEL PEAK 11(9P21.3) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-DA-A1IB 
       98.76        22.55         8.38        21.14        11.41        22.36 
TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A1A1 
       14.83         6.31        12.20        25.28        23.90        78.44 
TCGA-GN-A267 
       16.21 

  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                         1.02                          6.31 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        84.72                         98.76 
  DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE 
                        11.44                         21.14 
[1] "1.0 - 84.7 (11.4)" "6.3 - 98.8 (21.1)"
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK 11(9P21.3) WILD-TYPE" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A26D 
  "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK 11(9P21.3) WILD-TYPE" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A26D 
  "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q1                    TCGA-D3-A1Q5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q8 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A1Q9                    TCGA-D3-A2J6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A2J8                    TCGA-D3-A2J9 
"DEL PEAK 11(9P21.3) WILD-TYPE" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JD                    TCGA-D3-A2JK 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3C6                    TCGA-D3-A3CE 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-D9-A3Z1 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-D9-A3Z3                    TCGA-DA-A1HV 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A1I2                    TCGA-DA-A1IB 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-DA-A3F3                    TCGA-DA-A3F5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-DA-A3F8                    TCGA-EE-A17X 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A17Z                    TCGA-EE-A181 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A185 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A29C 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-EE-A29E 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29H                    TCGA-EE-A29L 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29N                    TCGA-EE-A29P 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29R                    TCGA-EE-A29S 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A29X 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-EE-A2A0                    TCGA-EE-A2A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2A6 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-ER-A19J 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19L                    TCGA-ER-A19M 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-ER-A19N                    TCGA-ER-A1A1 
  "DEL PEAK 11(9P21.3) MUTATED" "DEL PEAK 11(9P21.3) WILD-TYPE" 
                   TCGA-FR-A3YN                    TCGA-FR-A44A 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-FS-A4F9                    TCGA-FW-A3R5 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A264                    TCGA-GN-A265 
  "DEL PEAK 11(9P21.3) MUTATED"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A267                    TCGA-GN-A268 
"DEL PEAK 11(9P21.3) WILD-TYPE"   "DEL PEAK 11(9P21.3) MUTATED" 
                   TCGA-GN-A26D 
  "DEL PEAK 11(9P21.3) MUTATED" 
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P21.3) MUTATED     31   55
  DEL PEAK 11(9P21.3) WILD-TYPE    4   22
        clus
vv       DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  FEMALE                          31                             4
  MALE                            55                            22
                               vv
clus                            M0 M1 M1B M1C
  DEL PEAK 11(9P21.3) MUTATED   72  1   2   1
  DEL PEAK 11(9P21.3) WILD-TYPE 26  0   0   0
D29V4, multiclass
     clus
vv    DEL PEAK 11(9P21.3) MUTATED DEL PEAK 11(9P21.3) WILD-TYPE
  M0                           72                            26
  M1                            1                             0
  M1B                           2                             0
  M1C                           1                             0
                               vv
clus                            N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 11(9P21.3) MUTATED   45  1   2   8  1   0   6   1 11  2
  DEL PEAK 11(9P21.3) WILD-TYPE 16  0   1   2  0   3   2   0  2  0
D29V5, multiclass
D29V6, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 11(9P21.3) MUTATED             1       9        6        7       10
  DEL PEAK 11(9P21.3) WILD-TYPE           0       6        1        4        3
                               vv
clus                            STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 11(9P21.3) MUTATED           4         4         2         4
  DEL PEAK 11(9P21.3) WILD-TYPE         1         1         0         0
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(9P21.3) MUTATED            1          7         14        3
  DEL PEAK 11(9P21.3) WILD-TYPE          2          3          4        0
D29V7, multiclass

Clustering(30) Variable = Del Peak 12(10p15.3) mutation analysis
D30V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(10P15.3) MUTATED   10 20
  DEL PEAK 12(10P15.3) WILD-TYPE 17 12
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            30                             29 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                            20                             12 
$`DEL PEAK 12(10P15.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JD 
       16.47        32.55        98.76        28.08        10.26        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        13.32        24.00         2.86        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29H 
       13.68        17.56         6.31         1.12         4.27         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        1.08         9.47        12.03         9.99         6.48         8.09 
TCGA-EE-A2A2 TCGA-ER-A19L TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       23.90        12.99         5.95        31.33        16.21        15.39 

$`DEL PEAK 12(10P15.3) WILD-TYPE`
TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-D9-A3Z1 TCGA-DA-A1HV 
       22.55         8.38        21.14        15.25         4.01        48.79 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20F 
       22.36         7.00        14.83        11.57        12.20         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 
       37.97        11.15        38.63         8.84        11.31        25.28 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        8.94        11.11         4.18        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A26D 
       72.16        10.78         1.02        84.72        14.70 

  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                          1.08                           1.02 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                         98.76                          84.72 
  DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE 
                         12.51                          14.70 
[1] "1.1 - 98.8 (12.5)" "1.0 - 84.7 (14.7)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-GN-A26D 
"DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-GN-A26D 
"DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 12(10P15.3) WILD-TYPE"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 12(10P15.3) WILD-TYPE" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 12(10P15.3) MUTATED" "DEL PEAK 12(10P15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 12(10P15.3) MUTATED"   "DEL PEAK 12(10P15.3) MUTATED" 
                    TCGA-GN-A26D 
"DEL PEAK 12(10P15.3) WILD-TYPE" 
[1] "hr=" "2"  
D30V2, continuous
D30V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(10P15.3) MUTATED     20   35
  DEL PEAK 12(10P15.3) WILD-TYPE   15   42
        clus
vv       DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  FEMALE                           20                             15
  MALE                             35                             42
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 12(10P15.3) MUTATED   48  0   1   1
  DEL PEAK 12(10P15.3) WILD-TYPE 50  1   1   0
D30V4, multiclass
     clus
vv    DEL PEAK 12(10P15.3) MUTATED DEL PEAK 12(10P15.3) WILD-TYPE
  M0                            48                             50
  M1                             0                              1
  M1B                            1                              1
  M1C                            1                              0
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 12(10P15.3) MUTATED   28  1   3   6  0   0   3   1  7  1
  DEL PEAK 12(10P15.3) WILD-TYPE 33  0   0   4  1   3   5   0  6  1
D30V5, multiclass
D30V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 12(10P15.3) MUTATED             1       5        4        4        6
  DEL PEAK 12(10P15.3) WILD-TYPE           0      10        3        7        7
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 12(10P15.3) MUTATED           2         4         1         2
  DEL PEAK 12(10P15.3) WILD-TYPE         3         1         1         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(10P15.3) MUTATED            2          4         11        2
  DEL PEAK 12(10P15.3) WILD-TYPE          1          6          7        1
D30V7, multiclass

Clustering(31) Variable = Del Peak 13(10q23.31) mutation analysis
D31V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 13(10Q23.31) MUTATED   12 21
  DEL PEAK 13(10Q23.31) WILD-TYPE 15 11
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                             33                              26 
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                             21                              11 
$`DEL PEAK 13(10Q23.31) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JD 
       16.47        32.55        98.76        28.08        22.55        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HW 
        6.35        15.25        13.32        24.00         2.86        35.80 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 
       13.68        17.56        14.83         6.31         1.12         4.27 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29T 
        5.13        11.15         4.41         1.08        12.03         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19L TCGA-FR-A3YN 
        8.09        11.31        23.90         8.94        12.99         5.95 
TCGA-FR-A44A TCGA-GN-A264 TCGA-GN-A267 
       72.16        31.33        16.21 

$`DEL PEAK 13(10Q23.31) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
       10.26         8.38        21.14         4.01        48.79        51.12 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E 
       22.36         7.00        11.57        12.20        37.97        38.63 
TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 TCGA-ER-A19F TCGA-ER-A19J 
        9.47         8.84         9.99        25.28        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 
       28.64        42.84        78.44        10.78         1.02        84.72 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                           1.08                            1.02 
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                          98.76                           84.72 
  DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE 
                          12.99                           13.45 
[1] "1.1 - 98.8 (13.0)" "1.0 - 84.7 (13.4)"
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A264                      TCGA-GN-A265 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26D 
"DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A264                      TCGA-GN-A265 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26D 
"DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 13(10Q23.31) WILD-TYPE"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
  "DEL PEAK 13(10Q23.31) MUTATED"   "DEL PEAK 13(10Q23.31) MUTATED" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
"DEL PEAK 13(10Q23.31) WILD-TYPE" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A264                      TCGA-GN-A265 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 13(10Q23.31) MUTATED" "DEL PEAK 13(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26D 
"DEL PEAK 13(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.9"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 13(10Q23.31) MUTATED     26   38
  DEL PEAK 13(10Q23.31) WILD-TYPE    9   39
        clus
vv       DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE
  FEMALE                            26                               9
  MALE                              38                              39
                                 vv
clus                              M0 M1 M1B M1C
  DEL PEAK 13(10Q23.31) MUTATED   55  0   2   1
  DEL PEAK 13(10Q23.31) WILD-TYPE 43  1   0   0
D31V4, multiclass
     clus
vv    DEL PEAK 13(10Q23.31) MUTATED DEL PEAK 13(10Q23.31) WILD-TYPE
  M0                             55                              43
  M1                              0                               1
  M1B                             2                               0
  M1C                             1                               0
                                 vv
clus                              N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 13(10Q23.31) MUTATED   32  1   3   7  0   1   4   1  7  2
  DEL PEAK 13(10Q23.31) WILD-TYPE 29  0   0   3  1   2   4   0  6  0
D31V5, multiclass
D31V6, continuous
                                 vv
clus                              I OR II NOS STAGE I STAGE IA STAGE IB
  DEL PEAK 13(10Q23.31) MUTATED             1       6        6        5
  DEL PEAK 13(10Q23.31) WILD-TYPE           0       9        1        6
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 13(10Q23.31) MUTATED          8         2         3         1
  DEL PEAK 13(10Q23.31) WILD-TYPE        5         3         2         1
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 13(10Q23.31) MUTATED           3          2          6         10
  DEL PEAK 13(10Q23.31) WILD-TYPE         1          1          4          8
                                 vv
clus                              STAGE IV
  DEL PEAK 13(10Q23.31) MUTATED          2
  DEL PEAK 13(10Q23.31) WILD-TYPE        1
D31V7, multiclass

Clustering(32) Variable = Del Peak 14(11q23.1) mutation analysis
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(11Q23.1) MUTATED   16 19
  DEL PEAK 14(11Q23.1) WILD-TYPE 11 13
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                            35                             24 
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                            19                             13 
$`DEL PEAK 14(11Q23.1) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       11.41        15.25        24.00         2.86        48.79        35.80 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H 
        7.00        17.56         5.13        37.97        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A2 
        1.08         9.47         8.84         9.99         6.48        23.90 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A 
       11.11        12.99        28.64        42.84         5.95        72.16 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        14.70 

$`DEL PEAK 14(11Q23.1) WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D9-A3Z1 TCGA-DA-A1HY 
        8.38        21.14         6.35        13.32         4.01        51.12 
TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       13.68        22.36        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A0 
       12.20         4.27        38.63        12.03         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A1A1 TCGA-FS-A4F9 TCGA-FW-A3R5 
       25.28         8.94         4.18        78.44        10.78         1.02 

  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                          1.08                           1.02 
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                         98.76                          78.44 
  DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE 
                         15.39                          11.44 
[1] "1.1 - 98.8 (15.4)" "1.0 - 78.4 (11.4)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 14(11Q23.1) MUTATED" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 14(11Q23.1) WILD-TYPE" "DEL PEAK 14(11Q23.1) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 14(11Q23.1) MUTATED"   "DEL PEAK 14(11Q23.1) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 14(11Q23.1) MUTATED" 
[1] "hr=" "1.5"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q23.1) MUTATED     19   42
  DEL PEAK 14(11Q23.1) WILD-TYPE   16   35
        clus
vv       DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE
  FEMALE                           19                             16
  MALE                             42                             35
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 14(11Q23.1) MUTATED   51  0   2   1
  DEL PEAK 14(11Q23.1) WILD-TYPE 47  1   0   0
D32V4, multiclass
     clus
vv    DEL PEAK 14(11Q23.1) MUTATED DEL PEAK 14(11Q23.1) WILD-TYPE
  M0                            51                             47
  M1                             0                              1
  M1B                            2                              0
  M1C                            1                              0
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 14(11Q23.1) MUTATED   32  0   3   8  0   1   2   1  6  2
  DEL PEAK 14(11Q23.1) WILD-TYPE 29  1   0   2  1   2   6   0  7  0
D32V5, multiclass
D32V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 14(11Q23.1) MUTATED             1       7        5        6        6
  DEL PEAK 14(11Q23.1) WILD-TYPE           0       8        2        5        7
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 14(11Q23.1) MUTATED           1         3         1         0
  DEL PEAK 14(11Q23.1) WILD-TYPE         4         2         1         4
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 14(11Q23.1) MUTATED            2          8          8        2
  DEL PEAK 14(11Q23.1) WILD-TYPE          1          2         10        1
D32V7, multiclass

Clustering(33) Variable = Del Peak 15(12q24.33) mutation analysis
D33V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(12Q24.33) MUTATED    5  5
  DEL PEAK 15(12Q24.33) WILD-TYPE 22 27
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                             10                              49 
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                              5                              27 
$`DEL PEAK 15(12Q24.33) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-FS-A4F9 
       16.47        10.26         9.99         8.09        23.90        10.78 
TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.02        84.72        16.21        15.39 

$`DEL PEAK 15(12Q24.33) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        22.55         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB 
        2.86        48.79        35.80        51.12        13.68        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       12.20         4.27         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
        4.41         1.08         9.47        12.03         8.84         6.48 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       11.31        25.28         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A264 
       28.64        42.84        78.44         5.95        72.16        31.33 
TCGA-GN-A26D 
       14.70 

  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                           1.02                            1.08 
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                          84.72                           98.76 
  DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE 
                         13.085                          12.990 
[1] "1.0 - 84.7 (13.1)" "1.1 - 98.8 (13.0)"
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A264                      TCGA-GN-A265 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A26D 
"DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A264                      TCGA-GN-A265 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A26D 
"DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q1                      TCGA-D3-A1Q5 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q8 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A1Q9                      TCGA-D3-A2J6 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-D3-A2J8                      TCGA-D3-A2J9 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A2JD                      TCGA-D3-A2JK 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3C6                      TCGA-D3-A3CE 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D3-A3CF                      TCGA-D9-A3Z1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-D9-A3Z3                      TCGA-DA-A1HV 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A1I2                      TCGA-DA-A1IB 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F3                      TCGA-DA-A3F5 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-DA-A3F8                      TCGA-EE-A17X 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A17Z                      TCGA-EE-A181 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A185 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A29C 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29D                      TCGA-EE-A29E 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29H                      TCGA-EE-A29L 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29N                      TCGA-EE-A29P 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A29R                      TCGA-EE-A29S 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A29X 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-EE-A2A0                      TCGA-EE-A2A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-EE-A2A2                      TCGA-EE-A2A6 
  "DEL PEAK 15(12Q24.33) MUTATED" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19F                      TCGA-ER-A19J 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19L                      TCGA-ER-A19M 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-ER-A19N                      TCGA-ER-A1A1 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FR-A3YN                      TCGA-FR-A44A 
"DEL PEAK 15(12Q24.33) WILD-TYPE" "DEL PEAK 15(12Q24.33) WILD-TYPE" 
                     TCGA-FS-A4F9                      TCGA-FW-A3R5 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A264                      TCGA-GN-A265 
"DEL PEAK 15(12Q24.33) WILD-TYPE"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A267                      TCGA-GN-A268 
  "DEL PEAK 15(12Q24.33) MUTATED"   "DEL PEAK 15(12Q24.33) MUTATED" 
                     TCGA-GN-A26D 
"DEL PEAK 15(12Q24.33) WILD-TYPE" 
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12Q24.33) MUTATED      9   12
  DEL PEAK 15(12Q24.33) WILD-TYPE   26   65
        clus
vv       DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE
  FEMALE                             9                              26
  MALE                              12                              65
                                 vv
clus                              M0 M1 M1B M1C
  DEL PEAK 15(12Q24.33) MUTATED   17  0   0   1
  DEL PEAK 15(12Q24.33) WILD-TYPE 81  1   2   0
D33V4, multiclass
     clus
vv    DEL PEAK 15(12Q24.33) MUTATED DEL PEAK 15(12Q24.33) WILD-TYPE
  M0                             17                              81
  M1                              0                               1
  M1B                             0                               2
  M1C                             1                               0
                                 vv
clus                              N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 15(12Q24.33) MUTATED   12  0   1   1  1   0   0   1  2  0
  DEL PEAK 15(12Q24.33) WILD-TYPE 49  1   2   9  0   3   8   0 11  2
D33V5, multiclass
D33V6, continuous
                                 vv
clus                              I OR II NOS STAGE I STAGE IA STAGE IB
  DEL PEAK 15(12Q24.33) MUTATED             0       4        2        1
  DEL PEAK 15(12Q24.33) WILD-TYPE           1      11        5       10
                                 vv
clus                              STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(12Q24.33) MUTATED          2         1         2         0
  DEL PEAK 15(12Q24.33) WILD-TYPE       11         4         3         2
                                 vv
clus                              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(12Q24.33) MUTATED           1          1          1          2
  DEL PEAK 15(12Q24.33) WILD-TYPE         3          2          9         16
                                 vv
clus                              STAGE IV
  DEL PEAK 15(12Q24.33) MUTATED          1
  DEL PEAK 15(12Q24.33) WILD-TYPE        2
D33V7, multiclass

Clustering(34) Variable = Del Peak 16(13q34) mutation analysis
D34V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 16(13Q34) MUTATED    9  8
  DEL PEAK 16(13Q34) WILD-TYPE 18 24
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                          17                           42 
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                           8                           24 
$`DEL PEAK 16(13Q34) MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       28.08        22.55         8.38         2.86        48.79        35.80 
TCGA-DA-A1I2 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
       13.68        17.56         1.12        11.15        38.63         9.47 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-GN-A26D 
        6.48         8.94         5.95        10.78        14.70 

$`DEL PEAK 16(13Q34) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JD 
       16.47        32.55        98.76        10.26        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HY 
        6.35        15.25        13.32        24.00         4.01        51.12 
TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
       22.36         7.00        14.83        11.57         6.31        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P 
        4.27         5.13        37.97         4.41         1.08        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         8.09        11.31        25.28        23.90 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       72.16         1.02        31.33        84.72        16.21        15.39 

  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                        1.12                         1.02 
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                       48.79                        98.76 
  DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE 
                      11.150                       13.155 
[1] "1.1 - 48.8 (11.2)" "1.0 - 98.8 (13.2)"
                  TCGA-D3-A1Q1                   TCGA-D3-A1Q5 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q8 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-D3-A1Q9                   TCGA-D3-A2J6 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2J8                   TCGA-D3-A2J9 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2JD                   TCGA-D3-A2JK 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3C6                   TCGA-D3-A3CE 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-D9-A3Z1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D9-A3Z3                   TCGA-DA-A1HV 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A1I2                   TCGA-DA-A1IB 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A3F3                   TCGA-DA-A3F5 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A3F8                   TCGA-EE-A17X 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A17Z                   TCGA-EE-A181 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A183                   TCGA-EE-A185 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A29C 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-EE-A29E 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A29H                   TCGA-EE-A29L 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29N                   TCGA-EE-A29P 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29R                   TCGA-EE-A29S 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A29X 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A0                   TCGA-EE-A2A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A2                   TCGA-EE-A2A6 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-ER-A19J 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19M 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19N                   TCGA-ER-A1A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FR-A3YN                   TCGA-FR-A44A 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FS-A4F9                   TCGA-FW-A3R5 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A264                   TCGA-GN-A265 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A26D 
  "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-D3-A1Q1                   TCGA-D3-A1Q5 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q8 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-D3-A1Q9                   TCGA-D3-A2J6 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2J8                   TCGA-D3-A2J9 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2JD                   TCGA-D3-A2JK 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3C6                   TCGA-D3-A3CE 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-D9-A3Z1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D9-A3Z3                   TCGA-DA-A1HV 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A1I2                   TCGA-DA-A1IB 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A3F3                   TCGA-DA-A3F5 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A3F8                   TCGA-EE-A17X 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A17Z                   TCGA-EE-A181 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A183                   TCGA-EE-A185 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A29C 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-EE-A29E 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A29H                   TCGA-EE-A29L 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29N                   TCGA-EE-A29P 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29R                   TCGA-EE-A29S 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A29X 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A0                   TCGA-EE-A2A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A2                   TCGA-EE-A2A6 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-ER-A19J 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19M 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19N                   TCGA-ER-A1A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FR-A3YN                   TCGA-FR-A44A 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FS-A4F9                   TCGA-FW-A3R5 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A264                   TCGA-GN-A265 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A26D 
  "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-D3-A1Q1                   TCGA-D3-A1Q5 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q8 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-D3-A1Q9                   TCGA-D3-A2J6 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2J8                   TCGA-D3-A2J9 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A2JD                   TCGA-D3-A2JK 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3C6                   TCGA-D3-A3CE 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-D9-A3Z1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-D9-A3Z3                   TCGA-DA-A1HV 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A1I2                   TCGA-DA-A1IB 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-DA-A3F3                   TCGA-DA-A3F5 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-DA-A3F8                   TCGA-EE-A17X 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A17Z                   TCGA-EE-A181 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A183                   TCGA-EE-A185 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A29C 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-EE-A29E 
  "DEL PEAK 16(13Q34) MUTATED"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-EE-A29H                   TCGA-EE-A29L 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29N                   TCGA-EE-A29P 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29R                   TCGA-EE-A29S 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A29X 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A0                   TCGA-EE-A2A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-EE-A2A2                   TCGA-EE-A2A6 
"DEL PEAK 16(13Q34) WILD-TYPE"   "DEL PEAK 16(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-ER-A19J 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A19M 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-ER-A19N                   TCGA-ER-A1A1 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FR-A3YN                   TCGA-FR-A44A 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-FS-A4F9                   TCGA-FW-A3R5 
  "DEL PEAK 16(13Q34) MUTATED" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A264                   TCGA-GN-A265 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A267                   TCGA-GN-A268 
"DEL PEAK 16(13Q34) WILD-TYPE" "DEL PEAK 16(13Q34) WILD-TYPE" 
                  TCGA-GN-A26D 
  "DEL PEAK 16(13Q34) MUTATED" 
[1] "hr=" "1.1"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 16(13Q34) MUTATED      8   23
  DEL PEAK 16(13Q34) WILD-TYPE   27   54
        clus
vv       DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE
  FEMALE                          8                           27
  MALE                           23                           54
                              vv
clus                           M0 M1 M1B M1C
  DEL PEAK 16(13Q34) MUTATED   26  0   2   1
  DEL PEAK 16(13Q34) WILD-TYPE 72  1   0   0
D34V4, multiclass
     clus
vv    DEL PEAK 16(13Q34) MUTATED DEL PEAK 16(13Q34) WILD-TYPE
  M0                          26                           72
  M1                           0                            1
  M1B                          2                            0
  M1C                          1                            0
                              vv
clus                           N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 16(13Q34) MUTATED   17  0   0   4  0   1   2   1  4  1
  DEL PEAK 16(13Q34) WILD-TYPE 44  1   3   6  1   2   6   0  9  1
D34V5, multiclass
D34V6, continuous
                              vv
clus                           I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 16(13Q34) MUTATED             0       5        4        2        4
  DEL PEAK 16(13Q34) WILD-TYPE           1      10        3        9        9
                              vv
clus                           STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 16(13Q34) MUTATED           0         0         1         0
  DEL PEAK 16(13Q34) WILD-TYPE         5         5         1         4
                              vv
clus                           STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 16(13Q34) MUTATED            0          5          4        2
  DEL PEAK 16(13Q34) WILD-TYPE          3          5         14        1
D34V7, multiclass

Clustering(35) Variable = Del Peak 17(15q13.3) mutation analysis
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(15Q13.3) MUTATED    4  7
  DEL PEAK 17(15Q13.3) WILD-TYPE 23 25
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                            11                             48 
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                             7                             25 
$`DEL PEAK 17(15Q13.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-EE-A17Z 
       16.47        15.25        48.79        35.80        51.12         6.31 
TCGA-EE-A29L TCGA-EE-A29P TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
        1.08        12.03        31.33        16.21        14.70 

$`DEL PEAK 17(15Q13.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
        2.86        13.68        22.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C 
       11.57         1.12        12.20         4.27         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S 
       11.15        38.63         4.41         9.47         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 
        5.95        72.16        10.78         1.02        84.72        15.39 

  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                          1.08                           1.02 
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                         51.12                          98.76 
  DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE 
                         16.21                          11.49 
[1] "1.1 - 51.1 (16.2)" "1.0 - 98.8 (11.5)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 17(15Q13.3) MUTATED"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 17(15Q13.3) MUTATED"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 17(15Q13.3) MUTATED"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 17(15Q13.3) WILD-TYPE"   "DEL PEAK 17(15Q13.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 17(15Q13.3) WILD-TYPE" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 17(15Q13.3) MUTATED" "DEL PEAK 17(15Q13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 17(15Q13.3) MUTATED" 
[1] "hr=" "1.1"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(15Q13.3) MUTATED     11   14
  DEL PEAK 17(15Q13.3) WILD-TYPE   24   63
        clus
vv       DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE
  FEMALE                           11                             24
  MALE                             14                             63
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 17(15Q13.3) MUTATED   21  0   1   0
  DEL PEAK 17(15Q13.3) WILD-TYPE 77  1   1   1
D35V4, multiclass
     clus
vv    DEL PEAK 17(15Q13.3) MUTATED DEL PEAK 17(15Q13.3) WILD-TYPE
  M0                            21                             77
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 17(15Q13.3) MUTATED   13  0   1   1  0   0   3   0  4  1
  DEL PEAK 17(15Q13.3) WILD-TYPE 48  1   2   9  1   3   5   1  9  1
D35V5, multiclass
D35V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 17(15Q13.3) MUTATED             0       4        0        2        3
  DEL PEAK 17(15Q13.3) WILD-TYPE           1      11        7        9       10
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 17(15Q13.3) MUTATED           0         2         2         1
  DEL PEAK 17(15Q13.3) WILD-TYPE         5         3         0         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 17(15Q13.3) MUTATED            1          2          4        0
  DEL PEAK 17(15Q13.3) WILD-TYPE          2          8         14        3
D35V7, multiclass

Clustering(36) Variable = Del Peak 18(15q15.3) mutation analysis
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(15Q15.3) MUTATED    3 10
  DEL PEAK 18(15Q15.3) WILD-TYPE 24 22
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                            13                             46 
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                            10                             22 
$`DEL PEAK 18(15Q15.3) MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-EE-A17Z TCGA-EE-A181 
       16.47        15.25        48.79        35.80         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A29L TCGA-EE-A29P TCGA-ER-A19J TCGA-GN-A264 TCGA-GN-A267 
       12.20         1.08        12.03         4.18        31.33        16.21 
TCGA-GN-A26D 
       14.70 

$`DEL PEAK 18(15Q15.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14        11.41         6.35        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        2.86        51.12        13.68        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       14.83        11.57         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       38.63         4.41         9.47         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        8.09        11.31        25.28        23.90         8.94        11.11 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         5.95        72.16 
TCGA-FS-A4F9 TCGA-FW-A3R5 TCGA-GN-A265 TCGA-GN-A268 
       10.78         1.02        84.72        15.39 

  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                          1.08                           1.02 
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                         48.79                          98.76 
  DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE 
                         14.70                          12.28 
[1] "1.1 - 48.8 (14.7)" "1.0 - 98.8 (12.3)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 18(15Q15.3) MUTATED"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 18(15Q15.3) MUTATED"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 18(15Q15.3) MUTATED"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 18(15Q15.3) WILD-TYPE"   "DEL PEAK 18(15Q15.3) MUTATED" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 18(15Q15.3) WILD-TYPE" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 18(15Q15.3) MUTATED" "DEL PEAK 18(15Q15.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 18(15Q15.3) MUTATED" 
[1] "hr=" "1.6"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q15.3) MUTATED     12   14
  DEL PEAK 18(15Q15.3) WILD-TYPE   23   63
        clus
vv       DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE
  FEMALE                           12                             23
  MALE                             14                             63
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 18(15Q15.3) MUTATED   21  1   1   0
  DEL PEAK 18(15Q15.3) WILD-TYPE 77  0   1   1
D36V4, multiclass
     clus
vv    DEL PEAK 18(15Q15.3) MUTATED DEL PEAK 18(15Q15.3) WILD-TYPE
  M0                            21                             77
  M1                             1                              0
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 18(15Q15.3) MUTATED   15  0   1   1  0   0   3   0  4  0
  DEL PEAK 18(15Q15.3) WILD-TYPE 46  1   2   9  1   3   5   1  9  2
D36V5, multiclass
D36V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 18(15Q15.3) MUTATED             0       6        0        1        4
  DEL PEAK 18(15Q15.3) WILD-TYPE           1       9        7       10        9
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 18(15Q15.3) MUTATED           0         2         2         1
  DEL PEAK 18(15Q15.3) WILD-TYPE         5         3         0         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 18(15Q15.3) MUTATED            1          2          3        1
  DEL PEAK 18(15Q15.3) WILD-TYPE          2          8         15        2
D36V7, multiclass

Clustering(37) Variable = Del Peak 19(16p13.3) mutation analysis
D37V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(16P13.3) MUTATED    2 10
  DEL PEAK 19(16P13.3) WILD-TYPE 25 22
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                            12                             47 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                            10                             22 
$`DEL PEAK 19(16P13.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A181 TCGA-EE-A29D 
       32.55        22.55        35.80        13.68         1.12        11.15 
TCGA-EE-A29L TCGA-EE-A29X TCGA-EE-A2A0 TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A26D 
        1.08         8.09        11.31         1.02        16.21        14.70 

$`DEL PEAK 19(16P13.3) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
       11.41         6.35        15.25        13.32        24.00         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F5 
        2.86        48.79        51.12        22.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       14.83        11.57         6.31        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
       37.97        38.63         4.41         9.47        12.03         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F 
        9.99         6.48        25.28        23.90         8.94        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A3YN 
        4.18        12.99        28.64        42.84        78.44         5.95 
TCGA-FR-A44A TCGA-FS-A4F9 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       72.16        10.78        31.33        84.72        15.39 

  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                          1.02                           2.86 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                         35.80                          98.76 
  DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE 
                        12.495                         12.990 
[1] "1.0 - 35.8 (12.5)" "2.9 - 98.8 (13.0)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 19(16P13.3) WILD-TYPE"   "DEL PEAK 19(16P13.3) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
"DEL PEAK 19(16P13.3) WILD-TYPE" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 19(16P13.3) MUTATED" "DEL PEAK 19(16P13.3) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 19(16P13.3) MUTATED" 
[1] "hr=" "2.1"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16P13.3) MUTATED      9   13
  DEL PEAK 19(16P13.3) WILD-TYPE   26   64
        clus
vv       DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  FEMALE                            9                             26
  MALE                             13                             64
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 19(16P13.3) MUTATED   20  0   0   0
  DEL PEAK 19(16P13.3) WILD-TYPE 78  1   2   1
D37V4, multiclass
     clus
vv    DEL PEAK 19(16P13.3) MUTATED DEL PEAK 19(16P13.3) WILD-TYPE
  M0                            20                             78
  M1                             0                              1
  M1B                            0                              2
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 19(16P13.3) MUTATED   12  0   2   2  1   2   1   0  1  0
  DEL PEAK 19(16P13.3) WILD-TYPE 49  1   1   8  0   1   7   1 12  2
D37V5, multiclass
D37V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 19(16P13.3) MUTATED             1       3        1        1        2
  DEL PEAK 19(16P13.3) WILD-TYPE           0      12        6       10       11
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 19(16P13.3) MUTATED           2         1         1         1
  DEL PEAK 19(16P13.3) WILD-TYPE         3         4         1         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 19(16P13.3) MUTATED            2          3          3        0
  DEL PEAK 19(16P13.3) WILD-TYPE          1          7         15        3
D37V7, multiclass

Clustering(38) Variable = Del Peak 20(16q12.1) mutation analysis
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q12.1) MUTATED    9 14
  DEL PEAK 20(16Q12.1) WILD-TYPE 18 18
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                            23                             36 
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                            14                             18 
$`DEL PEAK 20(16Q12.1) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        98.76        10.26         2.86        35.80        13.68 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29C 
       17.56        14.83         6.31         1.12         4.27        37.97 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A0 
       11.15         1.08         9.47        12.03         8.09        11.31 
TCGA-ER-A19N TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26D 
       42.84         1.02        31.33        16.21        14.70 

$`DEL PEAK 20(16Q12.1) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       16.47        28.08        22.55         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV 
        6.35        15.25        13.32        24.00         4.01        48.79 
TCGA-DA-A1HY TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20F 
       51.12        22.36         7.00        11.57        12.20         5.13 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 
       38.63         4.41         8.84         9.99         6.48        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
       23.90         8.94        11.11         4.18        12.99        28.64 
TCGA-ER-A1A1 TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-GN-A265 TCGA-GN-A268 
       78.44         5.95        72.16        10.78        84.72        15.39 

  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                          1.02                           4.01 
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                         98.76                          84.72 
  DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE 
                        12.030                         13.155 
[1] "1.0 - 98.8 (12.0)" "4.0 - 84.7 (13.2)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q12.1) MUTATED"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 20(16Q12.1) WILD-TYPE" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 20(16Q12.1) WILD-TYPE"   "DEL PEAK 20(16Q12.1) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 20(16Q12.1) MUTATED" "DEL PEAK 20(16Q12.1) WILD-TYPE" 
                    TCGA-GN-A26D 
  "DEL PEAK 20(16Q12.1) MUTATED" 
[1] "hr=" "1.3"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q12.1) MUTATED     13   25
  DEL PEAK 20(16Q12.1) WILD-TYPE   22   52
        clus
vv       DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE
  FEMALE                           13                             22
  MALE                             25                             52
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 20(16Q12.1) MUTATED   32  0   1   0
  DEL PEAK 20(16Q12.1) WILD-TYPE 66  1   1   1
D38V4, multiclass
     clus
vv    DEL PEAK 20(16Q12.1) MUTATED DEL PEAK 20(16Q12.1) WILD-TYPE
  M0                            32                             66
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 20(16Q12.1) MUTATED   21  0   2   3  1   1   2   0  4  0
  DEL PEAK 20(16Q12.1) WILD-TYPE 40  1   1   7  0   2   6   1  9  2
D38V5, multiclass
D38V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 20(16Q12.1) MUTATED             1       3        1        3        6
  DEL PEAK 20(16Q12.1) WILD-TYPE           0      12        6        8        7
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 20(16Q12.1) MUTATED           1         3         2         1
  DEL PEAK 20(16Q12.1) WILD-TYPE         4         2         0         3
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 20(16Q12.1) MUTATED            2          4          5        0
  DEL PEAK 20(16Q12.1) WILD-TYPE          1          6         13        3
D38V7, multiclass

Clustering(39) Variable = Del Peak 21(16q24.2) mutation analysis
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(16Q24.2) MUTATED    8 17
  DEL PEAK 21(16Q24.2) WILD-TYPE 19 15
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                            25                             34 
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                            17                             15 
$`DEL PEAK 21(16Q24.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3CE TCGA-D9-A3Z3 
       32.55        98.76        22.55        10.26        13.32         2.86 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       35.80        13.68        14.83         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A0 
        4.27        11.15         4.41        12.03         8.09        11.31 
TCGA-ER-A19F TCGA-ER-A19N TCGA-FW-A3R5 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       11.11        42.84         1.02        31.33        16.21        15.39 
TCGA-GN-A26D 
       14.70 

$`DEL PEAK 21(16Q24.2) WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       16.47        28.08         8.38        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1IB 
       15.25        24.00         4.01        48.79        51.12        22.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
        7.00        17.56        11.57         5.13        37.97        38.63 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 
        1.08         9.47         8.84         9.99         6.48        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A1A1 
       23.90         8.94         4.18        12.99        28.64        78.44 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 TCGA-GN-A265 
        5.95        72.16        10.78        84.72 

  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                          1.02                           1.08 
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                         98.76                          84.72 
  DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE 
                         12.20                          14.12 
[1] "1.0 - 98.8 (12.2)" "1.1 - 84.7 (14.1)"
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A1Q1                     TCGA-D3-A1Q5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q8 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A1Q9                     TCGA-D3-A2J6 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A2J8                     TCGA-D3-A2J9 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A2JD                     TCGA-D3-A2JK 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D3-A3C6                     TCGA-D3-A3CE 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-D9-A3Z1 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-D9-A3Z3                     TCGA-DA-A1HV 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A1I2                     TCGA-DA-A1IB 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F3                     TCGA-DA-A3F5 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-DA-A3F8                     TCGA-EE-A17X 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A17Z                     TCGA-EE-A181 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A185 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A29C 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-EE-A29E 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29H                     TCGA-EE-A29L 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29N                     TCGA-EE-A29P 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A29R                     TCGA-EE-A29S 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A29X 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-EE-A2A0                     TCGA-EE-A2A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-EE-A2A2                     TCGA-EE-A2A6 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-ER-A19J 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19L                     TCGA-ER-A19M 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-ER-A19N                     TCGA-ER-A1A1 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FR-A3YN                     TCGA-FR-A44A 
"DEL PEAK 21(16Q24.2) WILD-TYPE" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-FS-A4F9                     TCGA-FW-A3R5 
"DEL PEAK 21(16Q24.2) WILD-TYPE"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A264                     TCGA-GN-A265 
  "DEL PEAK 21(16Q24.2) MUTATED" "DEL PEAK 21(16Q24.2) WILD-TYPE" 
                    TCGA-GN-A267                     TCGA-GN-A268 
  "DEL PEAK 21(16Q24.2) MUTATED"   "DEL PEAK 21(16Q24.2) MUTATED" 
                    TCGA-GN-A26D 
  "DEL PEAK 21(16Q24.2) MUTATED" 
[1] "hr=" "1.8"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q24.2) MUTATED     17   26
  DEL PEAK 21(16Q24.2) WILD-TYPE   18   51
        clus
vv       DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE
  FEMALE                           17                             18
  MALE                             26                             51
                                vv
clus                             M0 M1 M1B M1C
  DEL PEAK 21(16Q24.2) MUTATED   37  0   1   0
  DEL PEAK 21(16Q24.2) WILD-TYPE 61  1   1   1
D39V4, multiclass
     clus
vv    DEL PEAK 21(16Q24.2) MUTATED DEL PEAK 21(16Q24.2) WILD-TYPE
  M0                            37                             61
  M1                             0                              1
  M1B                            1                              1
  M1C                            0                              1
                                vv
clus                             N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  DEL PEAK 21(16Q24.2) MUTATED   24  0   2   5  1   3   2   0  2  0
  DEL PEAK 21(16Q24.2) WILD-TYPE 37  1   1   5  0   0   6   1 11  2
D39V5, multiclass
D39V6, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 21(16Q24.2) MUTATED             1       5        2        2        5
  DEL PEAK 21(16Q24.2) WILD-TYPE           0      10        5        9        8
                                vv
clus                             STAGE IIA STAGE IIB STAGE IIC STAGE III
  DEL PEAK 21(16Q24.2) MUTATED           1         5         2         2
  DEL PEAK 21(16Q24.2) WILD-TYPE         4         0         0         2
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 21(16Q24.2) MUTATED            2          6          3        0
  DEL PEAK 21(16Q24.2) WILD-TYPE          1          4         15        3
D39V7, multiclass
                   V1.D                      V2                      V3 
        "Time to Death"                   "AGE"                "GENDER" 
                     V4                      V5                      V6 
   "DISTANT.METASTASIS" "LYMPH.NODE.METASTASIS"       "TUMOR.STAGECODE" 
                     V7 
"NEOPLASM.DISEASESTAGE" 
> q(save="no")
