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

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

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

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

> source("/xchip/tcga/gdac_prod/applications/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/404262/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215663/SKCM-BRAF_Hotspot_Mutants.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-BRAF_Hotspot_Mutants", "-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-BRAF_Hotspot_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=67, in cluster file=99, common to both=67
[1] 36 67
[1] "Amp Peak  1(1q43) mutation analysis"
[1] 3
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                         34                          33 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                         34                          33 
[1] "Amp Peak  2(2q36.2) mutation analysis"
[1] 3
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                           18                            49 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                           18                            49 
[1] "Amp Peak  3(3p13) mutation analysis"
[1] 3
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         17                          50 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         17                          50 
[1] "Amp Peak  4(5p15.33) mutation analysis"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            24                             43 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            24                             43 
[1] "Amp Peak  5(6p25.3) mutation analysis"
[1] 3
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           32                            35 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           32                            35 
[1] "Amp Peak  6(7q21.11) mutation analysis"
[1] 3
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            49                             18 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            49                             18 
[1] "Amp Peak  7(7q34) mutation analysis"
[1] 3
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         55                          12 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         55                          12 
[1] "Amp Peak  8(8q21.13) mutation analysis"
[1] 3
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            36                             31 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            36                             31 
[1] "Amp Peak  9(8q24.21) mutation analysis"
[1] 3
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            37                             30 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            37                             30 
[1] "Amp Peak 10(12q15) mutation analysis"
[1] 3
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                          10                           57 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                          10                           57 
[1] "Amp Peak 11(15q26.2) mutation analysis"
[1] 3
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                            24                             43 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                            24                             43 
[1] "Amp Peak 12(17q24.3) mutation analysis"
[1] 3
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                            24                             43 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                            24                             43 
[1] "Amp Peak 13(19p13.2) mutation analysis"
[1] 3
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                            17                             50 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                            17                             50 
[1] "Amp Peak 14(22q13.32) mutation analysis"
[1] 3
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                             28                              39 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                             28                              39 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            20                             47 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            20                             47 
[1] "Del Peak  2(1p22.1) mutation analysis"
[1] 3
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           24                            43 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           24                            43 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           18                            49 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           18                            49 
[1] "Del Peak  4(3p26.1) mutation analysis"
[1] 3
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                           16                            51 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                           16                            51 
[1] "Del Peak  5(3q27.2) mutation analysis"
[1] 3
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                           13                            54 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                           13                            54 
[1] "Del Peak  6(4p16.3) mutation analysis"
[1] 3
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           15                            52 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           15                            52 
[1] "Del Peak  7(4q34.3) mutation analysis"
[1] 3
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           18                            49 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           18                            49 
[1] "Del Peak  8(5q11.2) mutation analysis"
[1] 3
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           24                            43 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           24                            43 
[1] "Del Peak  9(5q31.3) mutation analysis"
[1] 3
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           32                            35 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           32                            35 
[1] "Del Peak 10(6q25.2) mutation analysis"
[1] 3
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           45                            22 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           45                            22 
[1] "Del Peak 11(6q27) mutation analysis"
[1] 3
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         44                          23 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         44                          23 
[1] "Del Peak 12(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           54                            13 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           54                            13 
[1] "Del Peak 13(9q21.2) mutation analysis"
[1] 3
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                           34                            33 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                           34                            33 
[1] "Del Peak 14(10q21.1) mutation analysis"
[1] 3
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            48                             19 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            48                             19 
[1] "Del Peak 15(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             51                              16 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             51                              16 
[1] "Del Peak 16(11q22.3) mutation analysis"
[1] 3
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            36                             31 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            36                             31 
[1] "Del Peak 17(12q24.32) mutation analysis"
[1] 3
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                             11                              56 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                             11                              56 
[1] "Del Peak 18(14q31.1) mutation analysis"
[1] 3
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            23                             44 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            23                             44 
[1] "Del Peak 19(15q21.1) mutation analysis"
[1] 3
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             54 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             54 
[1] "Del Peak 20(16q23.3) mutation analysis"
[1] 3
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                            19                             48 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                            19                             48 
[1] "Del Peak 21(17q12) mutation analysis"
[1] 3
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                          19                           48 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                          19                           48 
[1] "Del Peak 22(19p13.3) mutation analysis"
[1] 3
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            24                             43 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            24                             43 
[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 67 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
          NA           NA         3687           NA           NA           NA 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
          NA           NA           NA           NA         4511          194 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA         3564           NA           NA           NA         3265 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        1861           NA         6553          477           NA         3335 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        2399           NA           NA         1455         1205          979 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
        1349         1716        10523         1787         1446         4134 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
        5536         1691          595           NA         3931           NA 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
          NA           NA           NA           NA         4403         7562 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
        3733          112           NA          714           NA           NA 
TCGA-ER-A19O TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
          NA           NA         3080           NA         4525         3664 
TCGA-GN-A265 
        2577 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=36,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "DISTANT.METASTASIS"     
[5] "LYMPH.NODE.METASTASIS"   "TUMOR.STAGECODE"        
[7] "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  2   1   5   1  11   6   2   2   7   3   1   2  10   1   7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 67 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=44, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1q43) mutation analysis
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1Q43) MUTATED   20 14
  AMP PEAK  1(1Q43) WILD-TYPE 12 20
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                         34                          32 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                         14                          20 
$`AMP PEAK  1(1Q43) MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX 
      121.22        23.77        11.87        60.23         9.30         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 
      117.17        20.38        35.93       107.34        61.18       215.44 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
      109.64       168.26        39.62        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M7 
       58.75        47.54       135.91       182.01        55.59        28.80 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX 
      248.61       122.73         3.68        23.47       138.77        48.59 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      357.37        53.52        15.45        32.71 

$`AMP PEAK  1(1Q43) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 
      112.54        71.80        31.59        12.10        58.03       148.31 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F 
       36.03       176.55        53.92        15.68        26.86        78.87 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       63.32        47.84        32.19        19.56        21.67       129.24 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AF 
       19.76       103.27       103.17        16.96       144.76        13.81 
TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        6.41       228.59         7.76       101.26        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                       3.68                        6.41 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                     357.37                      228.59 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                     56.005                      55.975 
[1] "3.7 - 357.4 (56.0)" "6.4 - 228.6 (56.0)"
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  1(1Q43) WILD-TYPE"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  1(1Q43) MUTATED"   "AMP PEAK  1(1Q43) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  1(1Q43) MUTATED" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  1(1Q43) WILD-TYPE" "AMP PEAK  1(1Q43) WILD-TYPE" 
[1] "hr=" "1.9"
D1V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  1(1Q43) MUTATED                    4             1
  AMP PEAK  1(1Q43) WILD-TYPE                  2             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  1(1Q43) MUTATED                                                                                          7
  AMP PEAK  1(1Q43) WILD-TYPE                                                                                        5
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  1(1Q43) MUTATED                    22
  AMP PEAK  1(1Q43) WILD-TYPE                  26
D1V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  1(1Q43) MUTATED
  DISTANT METASTASIS                                                                                               4
  PRIMARY TUMOR                                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         7
  REGIONAL LYMPH NODE                                                                                             22
                                                                                          clus
vv                                                                                         AMP PEAK  1(1Q43) WILD-TYPE
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                               26
D1V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1Q43) MUTATED     13   21
  AMP PEAK  1(1Q43) WILD-TYPE    9   24
        clus
vv       AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE
  FEMALE                        13                           9
  MALE                          21                          24
                             vv
clus                          M0 M1 M1A M1B M1C
  AMP PEAK  1(1Q43) MUTATED   28  0   1   0   2
  AMP PEAK  1(1Q43) WILD-TYPE 28  1   0   1   0
D1V5, multiclass
                             vv
clus                          N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  1(1Q43) MUTATED   17  0   1   3   0   2   2  4  2
  AMP PEAK  1(1Q43) WILD-TYPE 16  1   1   4   1   3   1  3  0
D1V6, multiclass
D1V7, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  1(1Q43) MUTATED             1       5        1        3        3
  AMP PEAK  1(1Q43) WILD-TYPE           1       5        1        2        5
                             vv
clus                          STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  1(1Q43) MUTATED           1         2         2          1
  AMP PEAK  1(1Q43) WILD-TYPE         2         0         3          1
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  1(1Q43) MUTATED            3          5        2
  AMP PEAK  1(1Q43) WILD-TYPE          4          4        1
D1V8, multiclass

Clustering(2) Variable = Amp Peak  2(2q36.2) mutation analysis
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(2Q36.2) MUTATED   10  8
  AMP PEAK  2(2Q36.2) WILD-TYPE 22 26
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                           18                            48 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                            8                            26 
$`AMP PEAK  2(2Q36.2) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D9-A148 TCGA-DA-A1HY TCGA-DA-A1I8 
       71.80        31.59        11.87       148.31       117.17        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29T 
      215.44        15.68       168.26        63.32        44.35       345.96 
TCGA-EE-A2A6 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A3AG TCGA-FS-A1ZD TCGA-FS-A1ZM 
       58.75       129.24        28.80        23.47        53.52       101.26 

$`AMP PEAK  2(2Q36.2) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
      112.54       121.22        23.77        12.10        58.03        60.23 
TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30         6.38        36.03        20.38       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
      107.34        61.18        26.86       109.64        78.87        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       39.62        32.19        56.42        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        21.67        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71        11.41       148.77       120.46        84.72 

  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                        11.87                          3.68 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                       345.96                        357.37 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                       61.035                        52.090 
[1] "11.9 - 346.0 (61.0)" "3.7 - 357.4 (52.1)" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  2(2Q36.2) MUTATED"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "AMP PEAK  2(2Q36.2) MUTATED" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"AMP PEAK  2(2Q36.2) WILD-TYPE"   "AMP PEAK  2(2Q36.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  2(2Q36.2) WILD-TYPE" "AMP PEAK  2(2Q36.2) WILD-TYPE" 
[1] "hr=" "1.4"
D2V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  2(2Q36.2) MUTATED                    2             1
  AMP PEAK  2(2Q36.2) WILD-TYPE                  4             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  2(2Q36.2) MUTATED                                                                                          4
  AMP PEAK  2(2Q36.2) WILD-TYPE                                                                                        8
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  2(2Q36.2) MUTATED                    11
  AMP PEAK  2(2Q36.2) WILD-TYPE                  37
D2V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  2(2Q36.2) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                               11
                                                                                          clus
vv                                                                                         AMP PEAK  2(2Q36.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   4
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             8
  REGIONAL LYMPH NODE                                                                                                 37
D2V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q36.2) MUTATED      3   15
  AMP PEAK  2(2Q36.2) WILD-TYPE   19   30
        clus
vv       AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE
  FEMALE                           3                            19
  MALE                            15                            30
                               vv
clus                            M0 M1 M1A M1B M1C
  AMP PEAK  2(2Q36.2) MUTATED   16  0   0   1   0
  AMP PEAK  2(2Q36.2) WILD-TYPE 40  1   1   0   2
D2V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  2(2Q36.2) MUTATED    6  0   1   2   1   1   1  4  1
  AMP PEAK  2(2Q36.2) WILD-TYPE 27  1   1   5   0   4   2  3  1
D2V6, multiclass
D2V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  2(2Q36.2) MUTATED             0       2        1        1        1
  AMP PEAK  2(2Q36.2) WILD-TYPE           2       8        1        4        7
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  2(2Q36.2) MUTATED           1         0         2          1
  AMP PEAK  2(2Q36.2) WILD-TYPE         2         2         3          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  2(2Q36.2) MUTATED            2          4        0
  AMP PEAK  2(2Q36.2) WILD-TYPE          5          5        3
D2V8, multiclass

Clustering(3) Variable = Amp Peak  3(3p13) mutation analysis
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(3P13) MUTATED   12  5
  AMP PEAK  3(3P13) WILD-TYPE 20 29
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         17                          49 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                          5                          29 
$`AMP PEAK  3(3P13) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F5 
       31.59        60.23        36.03        35.93       107.34       215.44 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       15.68       109.64        78.87        32.19        44.35       345.96 
TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-GN-A265 
      182.01        21.67       129.24       248.61        84.72 

$`AMP PEAK  3(3P13) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        23.77        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       58.03         9.30       148.31         6.38       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A 
      176.55        61.18        53.92        26.86       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       47.84        39.62        56.42        58.75        47.54       135.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
       16.96       144.76       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 
      120.46 

  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                      15.68                        3.68 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                     345.96                      357.37 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                      78.87                       53.92 
[1] "15.7 - 346.0 (78.9)" "3.7 - 357.4 (53.9)" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"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-A1I0                  TCGA-DA-A1I2 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"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-A1I0                  TCGA-DA-A1I2 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
"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-A1I0                  TCGA-DA-A1I2 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  3(3P13) MUTATED"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  3(3P13) MUTATED" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
"AMP PEAK  3(3P13) WILD-TYPE" "AMP PEAK  3(3P13) WILD-TYPE" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  3(3P13) WILD-TYPE"   "AMP PEAK  3(3P13) MUTATED" 
[1] "hr=" "2.7"
D3V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  3(3P13) MUTATED                    1             1
  AMP PEAK  3(3P13) WILD-TYPE                  5             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  3(3P13) MUTATED                                                                                          2
  AMP PEAK  3(3P13) WILD-TYPE                                                                                       10
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  3(3P13) MUTATED                    13
  AMP PEAK  3(3P13) WILD-TYPE                  35
D3V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  3(3P13) MUTATED
  DISTANT METASTASIS                                                                                               1
  PRIMARY TUMOR                                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         2
  REGIONAL LYMPH NODE                                                                                             13
                                                                                          clus
vv                                                                                         AMP PEAK  3(3P13) WILD-TYPE
  DISTANT METASTASIS                                                                                                 5
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          10
  REGIONAL LYMPH NODE                                                                                               35
D3V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(3P13) MUTATED      8    9
  AMP PEAK  3(3P13) WILD-TYPE   14   36
        clus
vv       AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE
  FEMALE                         8                          14
  MALE                           9                          36
                             vv
clus                          M0 M1 M1A M1B M1C
  AMP PEAK  3(3P13) MUTATED   15  0   0   0   1
  AMP PEAK  3(3P13) WILD-TYPE 41  1   1   1   1
D3V5, multiclass
                             vv
clus                          N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  3(3P13) MUTATED    9  0   0   2   1   2   0  1  1
  AMP PEAK  3(3P13) WILD-TYPE 24  1   2   5   0   3   3  6  1
D3V6, multiclass
D3V7, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  3(3P13) MUTATED             0       4        1        1        2
  AMP PEAK  3(3P13) WILD-TYPE           2       6        1        4        6
                             vv
clus                          STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  3(3P13) MUTATED           0         0         1          0
  AMP PEAK  3(3P13) WILD-TYPE         3         2         4          2
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  3(3P13) MUTATED            4          1        1
  AMP PEAK  3(3P13) WILD-TYPE          3          8        2
D3V8, multiclass

Clustering(4) Variable = Amp Peak  4(5p15.33) mutation analysis
D4V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  4(5P15.33) MUTATED   13 10
  AMP PEAK  4(5P15.33) WILD-TYPE 19 24
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            23                             43 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            10                             24 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 TCGA-DA-A1I2 
      112.54        31.59        12.10        58.03       148.31       176.55 
TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29M 
      107.34       215.44       109.64       168.26        39.62        44.35 
TCGA-EE-A29T TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD 
      345.96       129.24        28.80       248.61       122.73         3.68 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY TCGA-GN-A265 
       23.47       138.77        48.59       228.59        84.72 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO 
       71.80       121.22        23.77        11.87        60.23         9.30 
TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I7 
        6.38        36.03       117.17        20.38        35.93        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       53.92        15.68        26.86        78.87        63.32        47.84 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       32.19        56.42        58.75        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        21.67        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AF TCGA-ER-A19J TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       16.96       144.76        13.81         6.41         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
       53.52        15.45        32.71       101.26        11.41       148.77 
TCGA-GN-A262 
      120.46 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          3.68                           6.38 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        345.96                         357.37 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        109.64                          47.84 
[1] "3.7 - 346.0 (109.6)" "6.4 - 357.4 (47.8)" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  4(5P15.33) MUTATED"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
[1] "hr=" "2.1"
D4V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  4(5P15.33) MUTATED                    3             1
  AMP PEAK  4(5P15.33) WILD-TYPE                  3             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  4(5P15.33) MUTATED                                                                                          3
  AMP PEAK  4(5P15.33) WILD-TYPE                                                                                        9
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  4(5P15.33) MUTATED                    17
  AMP PEAK  4(5P15.33) WILD-TYPE                  31
D4V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  4(5P15.33) MUTATED
  DISTANT METASTASIS                                                                                                  3
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                17
                                                                                          clus
vv                                                                                         AMP PEAK  4(5P15.33) WILD-TYPE
  DISTANT METASTASIS                                                                                                    3
  PRIMARY TUMOR                                                                                                         0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              9
  REGIONAL LYMPH NODE                                                                                                  31
D4V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      8   16
  AMP PEAK  4(5P15.33) WILD-TYPE   14   29
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                            8                             14
  MALE                             16                             29
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK  4(5P15.33) MUTATED   18  0   0   1   1
  AMP PEAK  4(5P15.33) WILD-TYPE 38  1   1   0   1
D4V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  4(5P15.33) MUTATED   12  0   0   2   1   2   0  2  1
  AMP PEAK  4(5P15.33) WILD-TYPE 21  1   2   5   0   3   3  5  1
D4V6, multiclass
D4V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  4(5P15.33) MUTATED             1       4        0        2        3
  AMP PEAK  4(5P15.33) WILD-TYPE           1       6        2        3        5
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  4(5P15.33) MUTATED           1         0         0          0
  AMP PEAK  4(5P15.33) WILD-TYPE         2         2         5          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  4(5P15.33) MUTATED            3          3        1
  AMP PEAK  4(5P15.33) WILD-TYPE          4          6        2
D4V8, multiclass

Clustering(5) Variable = Amp Peak  5(6p25.3) mutation analysis
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(6P25.3) MUTATED   13 18
  AMP PEAK  5(6P25.3) WILD-TYPE 19 16
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           31                            35 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           18                            16 
$`AMP PEAK  5(6P25.3) MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 
      121.22        31.59        23.77        58.03        60.23       148.31 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A 
       20.38       176.55        35.93        26.86       168.26        63.32 
TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 
       56.42        47.54       182.01        55.59        19.56       129.24 
TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF 
       28.80       103.27       144.76       248.61         3.68        13.81 
TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZM 
       23.47         6.41        48.59       357.37        32.71       101.26 
TCGA-FS-A1ZR 
       11.41 

$`AMP PEAK  5(6P25.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3MO TCGA-D9-A1JX 
      112.54        71.80        11.87        12.10         9.30         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       36.03       117.17       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       15.68       109.64        78.87        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2M5 TCGA-EE-A2M8 
       44.35       345.96        58.75       135.91        21.67        19.76 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A3AB TCGA-EE-A3AH TCGA-FS-A1YY TCGA-FS-A1Z7 
      103.17        16.96       122.73       138.77       228.59         7.76 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       53.52        15.45       148.77       120.46        84.72 

  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                         3.68                          6.38 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                       357.37                        345.96 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                        55.59                         58.75 
[1] "3.7 - 357.4 (55.6)" "6.4 - 346.0 (58.8)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"AMP PEAK  5(6P25.3) WILD-TYPE"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "AMP PEAK  5(6P25.3) MUTATED" "AMP PEAK  5(6P25.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  5(6P25.3) MUTATED                    3             0
  AMP PEAK  5(6P25.3) WILD-TYPE                  3             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  5(6P25.3) MUTATED                                                                                          6
  AMP PEAK  5(6P25.3) WILD-TYPE                                                                                        6
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  5(6P25.3) MUTATED                    23
  AMP PEAK  5(6P25.3) WILD-TYPE                  25
D5V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  5(6P25.3) MUTATED
  DISTANT METASTASIS                                                                                                 3
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           6
  REGIONAL LYMPH NODE                                                                                               23
                                                                                          clus
vv                                                                                         AMP PEAK  5(6P25.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   3
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             6
  REGIONAL LYMPH NODE                                                                                                 25
D5V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P25.3) MUTATED     10   22
  AMP PEAK  5(6P25.3) WILD-TYPE   12   23
        clus
vv       AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE
  FEMALE                          10                            12
  MALE                            22                            23
                               vv
clus                            M0 M1 M1A M1B M1C
  AMP PEAK  5(6P25.3) MUTATED   25  1   1   1   1
  AMP PEAK  5(6P25.3) WILD-TYPE 31  0   0   0   1
D5V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  5(6P25.3) MUTATED   16  0   2   2   1   2   2  4  0
  AMP PEAK  5(6P25.3) WILD-TYPE 17  1   0   5   0   3   1  3  2
D5V6, multiclass
D5V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  5(6P25.3) MUTATED             1       7        0        3        3
  AMP PEAK  5(6P25.3) WILD-TYPE           1       3        2        2        5
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  5(6P25.3) MUTATED           1         1         2          2
  AMP PEAK  5(6P25.3) WILD-TYPE         2         1         3          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  5(6P25.3) MUTATED            3          3        2
  AMP PEAK  5(6P25.3) WILD-TYPE          4          6        1
D5V8, multiclass

Clustering(6) Variable = Amp Peak  6(7q21.11) mutation analysis
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(7Q21.11) MUTATED   23 25
  AMP PEAK  6(7Q21.11) WILD-TYPE  9  9
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            48                             18 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            25                              9 
$`AMP PEAK  6(7Q21.11) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
      112.54        71.80        31.59        23.77        11.87        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
        9.30       148.31         6.38        36.03       117.17       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       35.93       107.34        61.18        53.92       215.44        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       26.86       109.64       168.26        63.32        47.84        39.62 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       44.35        56.42       345.96        58.75        47.54       135.91 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AF 
      129.24        28.80        16.96       144.76       122.73        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       23.47       138.77         6.41        48.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       53.52        15.45       101.26        11.41       148.77        84.72 

$`AMP PEAK  6(7Q21.11) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1I0 TCGA-EE-A20F TCGA-EE-A29H 
      121.22        12.10        58.03        20.38        78.87        32.19 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME 
      182.01        55.59        19.56        21.67        19.76       103.27 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AD TCGA-FS-A1YY TCGA-FS-A1ZH TCGA-GN-A262 
      103.17       248.61         3.68       228.59        32.71       120.46 

  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                          6.38                           3.68 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                        357.37                         248.61 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                         55.17                          56.81 
[1] "6.4 - 357.4 (55.2)" "3.7 - 248.6 (56.8)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK  6(7Q21.11) WILD-TYPE" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  6(7Q21.11) MUTATED" "AMP PEAK  6(7Q21.11) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  6(7Q21.11) MUTATED"   "AMP PEAK  6(7Q21.11) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  6(7Q21.11) WILD-TYPE"   "AMP PEAK  6(7Q21.11) MUTATED" 
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  6(7Q21.11) MUTATED                    5             1
  AMP PEAK  6(7Q21.11) WILD-TYPE                  1             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  6(7Q21.11) MUTATED                                                                                         10
  AMP PEAK  6(7Q21.11) WILD-TYPE                                                                                        2
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  6(7Q21.11) MUTATED                    33
  AMP PEAK  6(7Q21.11) WILD-TYPE                  15
D6V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  6(7Q21.11) MUTATED
  DISTANT METASTASIS                                                                                                  5
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           10
  REGIONAL LYMPH NODE                                                                                                33
                                                                                          clus
vv                                                                                         AMP PEAK  6(7Q21.11) WILD-TYPE
  DISTANT METASTASIS                                                                                                    1
  PRIMARY TUMOR                                                                                                         0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
  REGIONAL LYMPH NODE                                                                                                  15
D6V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(7Q21.11) MUTATED     13   36
  AMP PEAK  6(7Q21.11) WILD-TYPE    9    9
        clus
vv       AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE
  FEMALE                           13                              9
  MALE                             36                              9
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK  6(7Q21.11) MUTATED   42  1   0   1   1
  AMP PEAK  6(7Q21.11) WILD-TYPE 14  0   1   0   1
D6V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  6(7Q21.11) MUTATED   21  0   2   7   1   4   2  6  2
  AMP PEAK  6(7Q21.11) WILD-TYPE 12  1   0   0   0   1   1  1  0
D6V6, multiclass
D6V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  6(7Q21.11) MUTATED             2       5        1        2        7
  AMP PEAK  6(7Q21.11) WILD-TYPE           0       5        1        3        1
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  6(7Q21.11) MUTATED           1         2         4          2
  AMP PEAK  6(7Q21.11) WILD-TYPE         2         0         1          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  6(7Q21.11) MUTATED            7          7        2
  AMP PEAK  6(7Q21.11) WILD-TYPE          0          2        1
D6V8, multiclass

Clustering(7) Variable = Amp Peak  7(7q34) mutation analysis
D7V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  7(7Q34) MUTATED   26 28
  AMP PEAK  7(7Q34) WILD-TYPE  6  6
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         54                          12 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         28                           6 
$`AMP PEAK  7(7Q34) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
      112.54        71.80        31.59        23.77        11.87        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30       148.31         6.38        36.03       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       15.68        26.86       109.64       168.26        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 
       47.54       135.91       182.01        19.56       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AF TCGA-EE-A3AG 
       19.76        16.96       144.76       122.73        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      138.77         6.41        48.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       15.45        32.71       101.26        11.41       148.77        84.72 

$`AMP PEAK  7(7Q34) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-EE-A20F TCGA-EE-A2GS TCGA-EE-A2M5 
      121.22        12.10        58.03        78.87        55.59        21.67 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AD TCGA-FS-A1YY TCGA-GN-A262 
      103.27       103.17       248.61         3.68       228.59       120.46 

  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                       6.38                        3.68 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                     357.37                      248.61 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                     51.055                      91.020 
[1] "6.4 - 357.4 (51.1)" "3.7 - 248.6 (91.0)"
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  7(7Q34) WILD-TYPE" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  7(7Q34) WILD-TYPE" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"AMP PEAK  7(7Q34) WILD-TYPE" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "AMP PEAK  7(7Q34) MUTATED" "AMP PEAK  7(7Q34) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "AMP PEAK  7(7Q34) MUTATED"   "AMP PEAK  7(7Q34) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"AMP PEAK  7(7Q34) WILD-TYPE"   "AMP PEAK  7(7Q34) MUTATED" 
[1] "hr=" "1.3"
D7V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  7(7Q34) MUTATED                    5             1
  AMP PEAK  7(7Q34) WILD-TYPE                  1             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  7(7Q34) MUTATED                                                                                         11
  AMP PEAK  7(7Q34) WILD-TYPE                                                                                        1
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  7(7Q34) MUTATED                    38
  AMP PEAK  7(7Q34) WILD-TYPE                  10
D7V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  7(7Q34) MUTATED
  DISTANT METASTASIS                                                                                               5
  PRIMARY TUMOR                                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                        11
  REGIONAL LYMPH NODE                                                                                             38
                                                                                          clus
vv                                                                                         AMP PEAK  7(7Q34) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                               10
D7V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(7Q34) MUTATED     16   39
  AMP PEAK  7(7Q34) WILD-TYPE    6    6
        clus
vv       AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE
  FEMALE                        16                           6
  MALE                          39                           6
                             vv
clus                          M0 M1 M1A M1B M1C
  AMP PEAK  7(7Q34) MUTATED   46  1   1   1   2
  AMP PEAK  7(7Q34) WILD-TYPE 10  0   0   0   0
D7V5, multiclass
                             vv
clus                          N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  7(7Q34) MUTATED   24  1   2   7   1   4   3  7  2
  AMP PEAK  7(7Q34) WILD-TYPE  9  0   0   0   0   1   0  0  0
D7V6, multiclass
D7V7, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  7(7Q34) MUTATED             2       6        2        2        7
  AMP PEAK  7(7Q34) WILD-TYPE           0       4        0        3        1
                             vv
clus                          STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  7(7Q34) MUTATED           2         2         5          2
  AMP PEAK  7(7Q34) WILD-TYPE         1         0         0          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  7(7Q34) MUTATED            7          8        3
  AMP PEAK  7(7Q34) WILD-TYPE          0          1        0
D7V8, multiclass

Clustering(8) Variable = Amp Peak  8(8q21.13) mutation analysis
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(8Q21.13) MUTATED   16 20
  AMP PEAK  8(8Q21.13) WILD-TYPE 16 14
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            36                             30 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            20                             14 
$`AMP PEAK  8(8Q21.13) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO 
       71.80        31.59        11.87        58.03        60.23         9.30 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A20B 
       36.03        20.38       176.55        35.93       215.44       109.64 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH 
       47.84        39.62        32.19       345.96       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A3AB 
       55.59       129.24        28.80        19.76        16.96       122.73 
TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
        3.68        23.47         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
      357.37        53.52       101.26        11.41       148.77        84.72 

$`AMP PEAK  8(8Q21.13) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D9-A148 TCGA-D9-A1JX 
      112.54       121.22        23.77        12.10       148.31         6.38 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
      117.17       107.34        61.18        53.92        15.68        26.86 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 
       78.87       168.26        63.32        44.35        56.42        58.75 
TCGA-EE-A2GB TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MK 
       47.54        19.56        21.67       103.27       103.17       144.76 
TCGA-EE-A2MP TCGA-EE-A3AF TCGA-EE-A3AH TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-GN-A262 
      248.61        13.81       138.77        15.45        32.71       120.46 

  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                          3.68                           6.38 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                        357.37                         248.61 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                        51.055                         59.965 
[1] "3.7 - 357.4 (51.1)" "6.4 - 248.6 (60.0)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  8(8Q21.13) WILD-TYPE" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  8(8Q21.13) MUTATED" "AMP PEAK  8(8Q21.13) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  8(8Q21.13) MUTATED"   "AMP PEAK  8(8Q21.13) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  8(8Q21.13) WILD-TYPE"   "AMP PEAK  8(8Q21.13) MUTATED" 
[1] "hr=" "1.1"
D8V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  8(8Q21.13) MUTATED                    2             0
  AMP PEAK  8(8Q21.13) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  8(8Q21.13) MUTATED                                                                                          9
  AMP PEAK  8(8Q21.13) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  8(8Q21.13) MUTATED                    25
  AMP PEAK  8(8Q21.13) WILD-TYPE                  23
D8V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  8(8Q21.13) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            9
  REGIONAL LYMPH NODE                                                                                                25
                                                                                          clus
vv                                                                                         AMP PEAK  8(8Q21.13) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                  23
D8V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q21.13) MUTATED     10   26
  AMP PEAK  8(8Q21.13) WILD-TYPE   12   19
        clus
vv       AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE
  FEMALE                           10                             12
  MALE                             26                             19
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK  8(8Q21.13) MUTATED   30  1   1   0   0
  AMP PEAK  8(8Q21.13) WILD-TYPE 26  0   0   1   2
D8V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  8(8Q21.13) MUTATED   16  1   0   6   1   2   2  3  1
  AMP PEAK  8(8Q21.13) WILD-TYPE 17  0   2   1   0   3   1  4  1
D8V6, multiclass
D8V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  8(8Q21.13) MUTATED             1       4        1        3        5
  AMP PEAK  8(8Q21.13) WILD-TYPE           1       6        1        2        3
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  8(8Q21.13) MUTATED           2         0         5          0
  AMP PEAK  8(8Q21.13) WILD-TYPE         1         2         0          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  8(8Q21.13) MUTATED            4          5        1
  AMP PEAK  8(8Q21.13) WILD-TYPE          3          4        2
D8V8, multiclass

Clustering(9) Variable = Amp Peak  9(8q24.21) mutation analysis
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(8Q24.21) MUTATED   17 19
  AMP PEAK  9(8Q24.21) WILD-TYPE 15 15
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            36                             30 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            19                             15 
$`AMP PEAK  9(8Q24.21) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW 
       71.80        31.59        58.03        60.23         9.30        36.03 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A20B 
      117.17        20.38       176.55        35.93       215.44       109.64 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH 
       47.84        39.62        32.19       345.96       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MP 
       55.59       129.24        28.80        19.76        16.96       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
      122.73         3.68        23.47         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS 
        7.76       357.37        53.52       101.26        11.41       148.77 

$`AMP PEAK  9(8Q24.21) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D9-A148 
      112.54       121.22        23.77        11.87        12.10       148.31 
TCGA-D9-A1JX TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
        6.38       107.34        61.18        53.92        15.68        26.86 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 
       78.87       168.26        63.32        44.35        56.42        58.75 
TCGA-EE-A2GB TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MK 
       47.54        19.56        21.67       103.27       103.17       144.76 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-GN-A262 TCGA-GN-A265 
       13.81       138.77        15.45        32.71       120.46        84.72 

  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                          3.68                           6.38 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        357.37                         168.26 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        54.555                         57.585 
[1] "3.7 - 357.4 (54.6)" "6.4 - 168.3 (57.6)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK  9(8Q24.21) MUTATED" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK  9(8Q24.21) WILD-TYPE"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "AMP PEAK  9(8Q24.21) MUTATED"   "AMP PEAK  9(8Q24.21) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK  9(8Q24.21) WILD-TYPE" "AMP PEAK  9(8Q24.21) WILD-TYPE" 
[1] "hr=" "1.2"
D9V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK  9(8Q24.21) MUTATED                    2             0
  AMP PEAK  9(8Q24.21) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  9(8Q24.21) MUTATED                                                                                          9
  AMP PEAK  9(8Q24.21) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  9(8Q24.21) MUTATED                    26
  AMP PEAK  9(8Q24.21) WILD-TYPE                  22
D9V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  9(8Q24.21) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            9
  REGIONAL LYMPH NODE                                                                                                26
                                                                                          clus
vv                                                                                         AMP PEAK  9(8Q24.21) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                  22
D9V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED     11   26
  AMP PEAK  9(8Q24.21) WILD-TYPE   11   19
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  FEMALE                           11                             11
  MALE                             26                             19
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK  9(8Q24.21) MUTATED   32  1   1   0   0
  AMP PEAK  9(8Q24.21) WILD-TYPE 24  0   0   1   2
D9V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK  9(8Q24.21) MUTATED   17  1   0   6   1   2   2  4  1
  AMP PEAK  9(8Q24.21) WILD-TYPE 16  0   2   1   0   3   1  3  1
D9V6, multiclass
D9V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK  9(8Q24.21) MUTATED             1       5        1        3        5
  AMP PEAK  9(8Q24.21) WILD-TYPE           1       5        1        2        3
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK  9(8Q24.21) MUTATED           2         0         5          0
  AMP PEAK  9(8Q24.21) WILD-TYPE         1         2         0          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK  9(8Q24.21) MUTATED            5          5        1
  AMP PEAK  9(8Q24.21) WILD-TYPE          2          4        2
D9V8, multiclass

Clustering(10) Variable = Amp Peak 10(12q15) mutation analysis
D10V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 10(12Q15) MUTATED    5  5
  AMP PEAK 10(12Q15) WILD-TYPE 27 29
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                          10                           56 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                           5                           29 
$`AMP PEAK 10(12Q15) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EE-A2A6 
       71.80        31.59        58.03        36.03       215.44        58.75 
TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M5 TCGA-FS-A1ZM 
       47.54       182.01        21.67       101.26 

$`AMP PEAK 10(12Q15) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
      112.54       121.22        23.77        11.87        12.10        60.23 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        9.30       148.31         6.38       117.17        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
       35.93       107.34        61.18        53.92        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64        78.87       168.26        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GS 
       32.19        44.35        56.42       345.96       135.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       19.56       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       23.47       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS 
      357.37        53.52        15.45        32.71        11.41       148.77 
TCGA-GN-A262 TCGA-GN-A265 
      120.46        84.72 

  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                       21.67                         3.68 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                      215.44                       357.37 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                      58.390                       54.755 
[1] "21.7 - 215.4 (58.4)" "3.7 - 357.4 (54.8)" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
  "AMP PEAK 10(12Q15) MUTATED" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
"AMP PEAK 10(12Q15) WILD-TYPE"   "AMP PEAK 10(12Q15) MUTATED" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
"AMP PEAK 10(12Q15) WILD-TYPE" "AMP PEAK 10(12Q15) WILD-TYPE" 
[1] "hr=" "1.1"
D10V2, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 10(12Q15) MUTATED                    0             0
  AMP PEAK 10(12Q15) WILD-TYPE                  6             1
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 10(12Q15) MUTATED                                                                                          2
  AMP PEAK 10(12Q15) WILD-TYPE                                                                                       10
                              vv
clus                           REGIONAL LYMPH NODE
  AMP PEAK 10(12Q15) MUTATED                     8
  AMP PEAK 10(12Q15) WILD-TYPE                  40
D10V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 10(12Q15) MUTATED
  DISTANT METASTASIS                                                                                                0
  PRIMARY TUMOR                                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          2
  REGIONAL LYMPH NODE                                                                                               8
                                                                                          clus
vv                                                                                         AMP PEAK 10(12Q15) WILD-TYPE
  DISTANT METASTASIS                                                                                                  6
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           10
  REGIONAL LYMPH NODE                                                                                                40
D10V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 10(12Q15) MUTATED      2    8
  AMP PEAK 10(12Q15) WILD-TYPE   20   37
        clus
vv       AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE
  FEMALE                          2                           20
  MALE                            8                           37
                              vv
clus                           M0 M1 M1A M1B M1C
  AMP PEAK 10(12Q15) MUTATED   10  0   0   0   0
  AMP PEAK 10(12Q15) WILD-TYPE 46  1   1   1   2
D10V5, multiclass
                              vv
clus                           N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 10(12Q15) MUTATED    4  0   1   2   1   0   1  1  0
  AMP PEAK 10(12Q15) WILD-TYPE 29  1   1   5   0   5   2  6  2
D10V6, multiclass
D10V7, continuous
                              vv
clus                           I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 10(12Q15) MUTATED             0       2        1        1        0
  AMP PEAK 10(12Q15) WILD-TYPE           2       8        1        4        8
                              vv
clus                           STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 10(12Q15) MUTATED           0         0         2          1
  AMP PEAK 10(12Q15) WILD-TYPE         3         2         3          1
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 10(12Q15) MUTATED            2          1        0
  AMP PEAK 10(12Q15) WILD-TYPE          5          8        3
D10V8, multiclass

Clustering(11) Variable = Amp Peak 11(15q26.2) mutation analysis
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(15Q26.2) MUTATED   11 13
  AMP PEAK 11(15Q26.2) WILD-TYPE 21 21
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                            24                             42 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                            13                             21 
$`AMP PEAK 11(15Q26.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D9-A148 
      112.54        31.59        23.77        11.87        60.23       148.31 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       36.03        61.18       215.44        26.86        78.87       168.26 
TCGA-EE-A29T TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MP TCGA-EE-A3AB 
      345.96       182.01       129.24        28.80       248.61       122.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-GN-A265 
       13.81        23.47         7.76       357.37        53.52        84.72 

$`AMP PEAK 11(15Q26.2) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A1JX 
       71.80       121.22        12.10        58.03         9.30         6.38 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
      117.17        20.38       176.55        35.93       107.34        53.92 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       15.68       109.64        63.32        47.84        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS 
       44.35        56.42        58.75        47.54       135.91        55.59 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       19.56        21.67        19.76       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A3AD TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
      144.76         3.68       138.77         6.41        48.59       228.59 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
       15.45        32.71       101.26        11.41       148.77       120.46 

  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                          7.76                           3.68 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                        357.37                         228.59 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                        70.025                         51.255 
[1] "7.8 - 357.4 (70.0)" "3.7 - 228.6 (51.3)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 11(15Q26.2) MUTATED"   "AMP PEAK 11(15Q26.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 11(15Q26.2) MUTATED" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 11(15Q26.2) WILD-TYPE" "AMP PEAK 11(15Q26.2) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 11(15Q26.2) WILD-TYPE"   "AMP PEAK 11(15Q26.2) MUTATED" 
[1] "hr=" "1.4"
D11V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 11(15Q26.2) MUTATED                    2             0
  AMP PEAK 11(15Q26.2) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 11(15Q26.2) MUTATED                                                                                          2
  AMP PEAK 11(15Q26.2) WILD-TYPE                                                                                       10
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 11(15Q26.2) MUTATED                    20
  AMP PEAK 11(15Q26.2) WILD-TYPE                  28
D11V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 11(15Q26.2) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            2
  REGIONAL LYMPH NODE                                                                                                20
                                                                                          clus
vv                                                                                         AMP PEAK 11(15Q26.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             10
  REGIONAL LYMPH NODE                                                                                                  28
D11V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(15Q26.2) MUTATED      5   19
  AMP PEAK 11(15Q26.2) WILD-TYPE   17   26
        clus
vv       AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE
  FEMALE                            5                             17
  MALE                             19                             26
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK 11(15Q26.2) MUTATED   19  0   0   1   0
  AMP PEAK 11(15Q26.2) WILD-TYPE 37  1   1   0   2
D11V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 11(15Q26.2) MUTATED   10  0   0   4   1   1   0  3  1
  AMP PEAK 11(15Q26.2) WILD-TYPE 23  1   2   3   0   4   3  4  1
D11V6, multiclass
D11V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 11(15Q26.2) MUTATED             2       5        0        0        2
  AMP PEAK 11(15Q26.2) WILD-TYPE           0       5        2        5        6
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 11(15Q26.2) MUTATED           1         0         1          0
  AMP PEAK 11(15Q26.2) WILD-TYPE         2         2         4          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 11(15Q26.2) MUTATED            3          4        0
  AMP PEAK 11(15Q26.2) WILD-TYPE          4          5        3
D11V8, multiclass

Clustering(12) Variable = Amp Peak 12(17q24.3) mutation analysis
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(17Q24.3) MUTATED   15  9
  AMP PEAK 12(17Q24.3) WILD-TYPE 17 25
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                            24                             42 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                             9                             25 
$`AMP PEAK 12(17Q24.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HY 
       31.59        11.87        60.23         9.30       148.31       117.17 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H 
       61.18       215.44        78.87       168.26        47.84        32.19 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M7 TCGA-EE-A2MP 
       56.42        58.75        47.54       182.01        28.80       248.61 
TCGA-FS-A1YX TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A265 
       48.59        53.52        15.45       101.26       148.77        84.72 

$`AMP PEAK 12(17Q24.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54        71.80       121.22        23.77        12.10        58.03 
TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        6.38        36.03        20.38       176.55        35.93       107.34 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29E 
       53.92        15.68        26.86       109.64        63.32        39.62 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       44.35       345.96       135.91        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
      129.24        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-GN-A262 
      228.59         7.76       357.37        32.71        11.41       120.46 

  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                          9.30                           3.68 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                        248.61                         357.37 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                        59.490                         49.135 
[1] "9.3 - 248.6 (59.5)" "3.7 - 357.4 (49.1)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "AMP PEAK 12(17Q24.3) MUTATED" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 12(17Q24.3) MUTATED"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
[1] "hr=" "1.8"
D12V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 12(17Q24.3) MUTATED                    2             0
  AMP PEAK 12(17Q24.3) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 12(17Q24.3) MUTATED                                                                                          4
  AMP PEAK 12(17Q24.3) WILD-TYPE                                                                                        8
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 12(17Q24.3) MUTATED                    18
  AMP PEAK 12(17Q24.3) WILD-TYPE                  30
D12V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 12(17Q24.3) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            4
  REGIONAL LYMPH NODE                                                                                                18
                                                                                          clus
vv                                                                                         AMP PEAK 12(17Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              8
  REGIONAL LYMPH NODE                                                                                                  30
D12V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(17Q24.3) MUTATED      6   18
  AMP PEAK 12(17Q24.3) WILD-TYPE   16   27
        clus
vv       AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE
  FEMALE                            6                             16
  MALE                             18                             27
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK 12(17Q24.3) MUTATED   22  0   0   1   0
  AMP PEAK 12(17Q24.3) WILD-TYPE 34  1   1   0   2
D12V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 12(17Q24.3) MUTATED   13  0   1   2   1   1   2  3  0
  AMP PEAK 12(17Q24.3) WILD-TYPE 20  1   1   5   0   4   1  4  2
D12V6, multiclass
D12V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 12(17Q24.3) MUTATED             0       4        2        1        3
  AMP PEAK 12(17Q24.3) WILD-TYPE           2       6        0        4        5
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 12(17Q24.3) MUTATED           1         2         3          1
  AMP PEAK 12(17Q24.3) WILD-TYPE         2         0         2          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 12(17Q24.3) MUTATED            2          3        0
  AMP PEAK 12(17Q24.3) WILD-TYPE          5          6        3
D12V8, multiclass

Clustering(13) Variable = Amp Peak 13(19p13.2) mutation analysis
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(19P13.2) MUTATED    7 10
  AMP PEAK 13(19P13.2) WILD-TYPE 25 24
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                            17                             49 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                            10                             24 
$`AMP PEAK 13(19P13.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-DA-A1I0 TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29P 
      112.54        71.80        20.38       215.44        39.62        56.42 
TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MG TCGA-ER-A19J TCGA-FS-A1YY 
      182.01       129.24        28.80       103.17         6.41       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS 
        7.76       357.37        53.52       101.26       148.77 

$`AMP PEAK 13(19P13.2) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
      121.22        31.59        23.77        11.87        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       60.23         9.30       148.31         6.38        36.03       117.17 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 
      176.55        35.93       107.34        61.18        53.92        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       26.86       109.64        78.87       168.26        63.32        47.84 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       32.19        44.35       345.96        58.75        47.54       135.91 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH 
       55.59        19.56        21.67        19.76       103.27        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-GN-A262 
      138.77        48.59        15.45        32.71        11.41       120.46 
TCGA-GN-A265 
       84.72 

  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                          6.41                           3.68 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                        357.37                         345.96 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                        101.26                          48.59 
[1] "6.4 - 357.4 (101.3)" "3.7 - 346.0 (48.6)" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "AMP PEAK 13(19P13.2) MUTATED"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"AMP PEAK 13(19P13.2) WILD-TYPE"   "AMP PEAK 13(19P13.2) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
[1] "hr=" "1.3"
D13V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 13(19P13.2) MUTATED                    2             0
  AMP PEAK 13(19P13.2) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 13(19P13.2) MUTATED                                                                                          3
  AMP PEAK 13(19P13.2) WILD-TYPE                                                                                        9
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 13(19P13.2) MUTATED                    12
  AMP PEAK 13(19P13.2) WILD-TYPE                  36
D13V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 13(19P13.2) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                12
                                                                                          clus
vv                                                                                         AMP PEAK 13(19P13.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              9
  REGIONAL LYMPH NODE                                                                                                  36
D13V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(19P13.2) MUTATED      2   15
  AMP PEAK 13(19P13.2) WILD-TYPE   20   30
        clus
vv       AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE
  FEMALE                            2                             20
  MALE                             15                             30
                                vv
clus                             M0 M1 M1A M1B M1C
  AMP PEAK 13(19P13.2) MUTATED   15  1   1   0   0
  AMP PEAK 13(19P13.2) WILD-TYPE 41  0   0   1   2
D13V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 13(19P13.2) MUTATED   10  0   0   3   0   0   1  3  0
  AMP PEAK 13(19P13.2) WILD-TYPE 23  1   2   4   1   5   2  4  2
D13V6, multiclass
D13V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  AMP PEAK 13(19P13.2) MUTATED             2       3        0        0        2
  AMP PEAK 13(19P13.2) WILD-TYPE           0       7        2        5        6
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  AMP PEAK 13(19P13.2) MUTATED           2         1         2          0
  AMP PEAK 13(19P13.2) WILD-TYPE         1         1         3          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 13(19P13.2) MUTATED            1          3        1
  AMP PEAK 13(19P13.2) WILD-TYPE          6          6        2
D13V8, multiclass

Clustering(14) Variable = Amp Peak 14(22q13.32) mutation analysis
D14V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 14(22Q13.32) MUTATED   15 13
  AMP PEAK 14(22Q13.32) WILD-TYPE 17 21
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                             28                              38 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                             13                              21 
$`AMP PEAK 14(22Q13.32) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
       71.80        31.59        60.23         9.30       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20H 
       36.03        20.38        61.18        53.92       215.44       168.26 
TCGA-EE-A29M TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2M6 TCGA-EE-A2M7 
       44.35        58.75        47.54       182.01       129.24        28.80 
TCGA-EE-A2ME TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-FS-A1Z7 TCGA-FS-A1ZD 
      103.27       122.73         3.68        23.47         7.76        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A265 
       32.71       101.26       148.77        84.72 

$`AMP PEAK 14(22Q13.32) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54       121.22        23.77        11.87        12.10        58.03 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A183 
      117.17       176.55        35.93       107.34        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
      109.64        78.87        63.32        47.84        39.62        32.19 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       56.42       345.96       135.91        55.59        19.56        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AF 
       19.76       103.17        16.96       144.76       248.61        13.81 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF 
      138.77         6.41        48.59       228.59       357.37        15.45 
TCGA-FS-A1ZR TCGA-GN-A262 
       11.41       120.46 

  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                           3.68                            6.41 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                         215.44                          357.37 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                         56.335                          56.005 
[1] "3.7 - 215.4 (56.3)" "6.4 - 357.4 (56.0)"
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "AMP PEAK 14(22Q13.32) MUTATED" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "AMP PEAK 14(22Q13.32) MUTATED"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"AMP PEAK 14(22Q13.32) WILD-TYPE"   "AMP PEAK 14(22Q13.32) MUTATED" 
[1] "hr=" "1"  
D14V2, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 14(22Q13.32) MUTATED                    1             1
  AMP PEAK 14(22Q13.32) WILD-TYPE                  5             0
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 14(22Q13.32) MUTATED                                                                                          7
  AMP PEAK 14(22Q13.32) WILD-TYPE                                                                                        5
                                 vv
clus                              REGIONAL LYMPH NODE
  AMP PEAK 14(22Q13.32) MUTATED                    19
  AMP PEAK 14(22Q13.32) WILD-TYPE                  29
D14V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 14(22Q13.32) MUTATED
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             7
  REGIONAL LYMPH NODE                                                                                                 19
                                                                                          clus
vv                                                                                         AMP PEAK 14(22Q13.32) WILD-TYPE
  DISTANT METASTASIS                                                                                                     5
  PRIMARY TUMOR                                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               5
  REGIONAL LYMPH NODE                                                                                                   29
D14V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(22Q13.32) MUTATED      6   22
  AMP PEAK 14(22Q13.32) WILD-TYPE   16   23
        clus
vv       AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE
  FEMALE                             6                              16
  MALE                              22                              23
                                 vv
clus                              M0 M1 M1A M1B M1C
  AMP PEAK 14(22Q13.32) MUTATED   21  0   1   1   1
  AMP PEAK 14(22Q13.32) WILD-TYPE 35  1   0   0   1
D14V5, multiclass
                                 vv
clus                              N0 N1 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 14(22Q13.32) MUTATED    9  0   1   4   1   1   3  4  1
  AMP PEAK 14(22Q13.32) WILD-TYPE 24  1   1   3   0   4   0  3  1
D14V6, multiclass
D14V7, continuous
                                 vv
clus                              I OR II NOS STAGE I STAGE IA STAGE IB
  AMP PEAK 14(22Q13.32) MUTATED             0       4        1        1
  AMP PEAK 14(22Q13.32) WILD-TYPE           2       6        1        4
                                 vv
clus                              STAGE II STAGE IIA STAGE IIC STAGE III
  AMP PEAK 14(22Q13.32) MUTATED          2         1         0         4
  AMP PEAK 14(22Q13.32) WILD-TYPE        6         2         2         1
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 14(22Q13.32) MUTATED            1          3          4        1
  AMP PEAK 14(22Q13.32) WILD-TYPE          1          4          5        2
D14V8, multiclass

Clustering(15) Variable = Del Peak  1(1p36.31) mutation analysis
D15V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    9 11
  DEL PEAK  1(1P36.31) WILD-TYPE 23 23
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            20                             46 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            11                             23 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A1I2 
       12.10        58.03        60.23         6.38        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A2GE 
       61.18       215.44        15.68        78.87       168.26       135.91 
TCGA-EE-A2M5 TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-FS-A1YX 
       21.67       144.76       122.73         3.68        13.81        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 
      228.59         7.76 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30       148.31        36.03       117.17        35.93       107.34 
TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       53.92        26.86       109.64        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       32.19        44.35        56.42       345.96        58.75        47.54 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
      182.01        55.59        19.56       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AG TCGA-EE-A3AH 
      103.27       103.17        16.96       248.61        23.47       138.77 
TCGA-ER-A19J TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
        6.41       357.37        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          3.68                           6.41 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        228.59                         357.37 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        59.130                         54.755 
[1] "3.7 - 228.6 (59.1)" "6.4 - 357.4 (54.8)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK  1(1P36.31) MUTATED"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  1(1P36.31) MUTATED                    2             0
  DEL PEAK  1(1P36.31) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  1(1P36.31) MUTATED                                                                                          3
  DEL PEAK  1(1P36.31) WILD-TYPE                                                                                        9
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  1(1P36.31) MUTATED                    15
  DEL PEAK  1(1P36.31) WILD-TYPE                  33
D15V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P36.31) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                15
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P36.31) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              9
  REGIONAL LYMPH NODE                                                                                                  33
D15V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      7   13
  DEL PEAK  1(1P36.31) WILD-TYPE   15   32
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                            7                             15
  MALE                             13                             32
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK  1(1P36.31) MUTATED   16  0   1   0   0
  DEL PEAK  1(1P36.31) WILD-TYPE 40  1   0   1   2
D15V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  1(1P36.31) MUTATED    8  0   0   2   0   4   0  2  1
  DEL PEAK  1(1P36.31) WILD-TYPE 25  1   2   5   1   1   3  5  1
D15V6, multiclass
D15V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  1(1P36.31) MUTATED             0       4        0        1        2
  DEL PEAK  1(1P36.31) WILD-TYPE           2       6        2        4        6
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  1(1P36.31) MUTATED           1         0         1          0
  DEL PEAK  1(1P36.31) WILD-TYPE         2         2         4          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.31) MUTATED            2          5        0
  DEL PEAK  1(1P36.31) WILD-TYPE          5          4        3
D15V8, multiclass

Clustering(16) Variable = Del Peak  2(1p22.1) mutation analysis
D16V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P22.1) MUTATED   13 11
  DEL PEAK  2(1P22.1) WILD-TYPE 19 23
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           24                            42 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           11                            23 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1I0 TCGA-DA-A1I2 
       31.59        11.87        60.23         9.30        20.38       176.55 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20H 
       61.18        53.92       215.44        15.68       109.64       168.26 
TCGA-EE-A29C TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB 
       47.84       345.96       135.91       144.76       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZS TCGA-GN-A262 
        3.68       138.77        48.59         7.76       148.77       120.46 

$`DEL PEAK  2(1P22.1) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54        71.80       121.22        23.77        12.10        58.03 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 
      148.31         6.38        36.03       117.17        35.93       107.34 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       26.86        78.87        63.32        39.62        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       56.42        58.75        47.54       182.01        55.59        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       21.67       129.24        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1ZC 
       16.96        13.81        23.47         6.41       228.59       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A265 
       53.52        15.45        32.71       101.26        11.41        84.72 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         3.68                          6.38 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                       345.96                        357.37 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        85.41                         50.53 
[1] "3.7 - 346.0 (85.4)" "6.4 - 357.4 (50.5)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  2(1P22.1) MUTATED"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  2(1P22.1) WILD-TYPE"   "DEL PEAK  2(1P22.1) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
[1] "hr=" "1.5"
D16V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  2(1P22.1) MUTATED                    1             0
  DEL PEAK  2(1P22.1) WILD-TYPE                  5             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  2(1P22.1) MUTATED                                                                                          7
  DEL PEAK  2(1P22.1) WILD-TYPE                                                                                        5
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  2(1P22.1) MUTATED                    16
  DEL PEAK  2(1P22.1) WILD-TYPE                  32
D16V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  2(1P22.1) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           7
  REGIONAL LYMPH NODE                                                                                               16
                                                                                          clus
vv                                                                                         DEL PEAK  2(1P22.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                   5
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             5
  REGIONAL LYMPH NODE                                                                                                 32
D16V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P22.1) MUTATED      8   16
  DEL PEAK  2(1P22.1) WILD-TYPE   14   29
        clus
vv       DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE
  FEMALE                           8                            14
  MALE                            16                            29
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  2(1P22.1) MUTATED   20  0   1   0   0
  DEL PEAK  2(1P22.1) WILD-TYPE 36  1   0   1   2
D16V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  2(1P22.1) MUTATED    9  0   0   3   1   3   1  3  1
  DEL PEAK  2(1P22.1) WILD-TYPE 24  1   2   4   0   2   2  4  1
D16V6, multiclass
D16V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  2(1P22.1) MUTATED             0       4        0        1        4
  DEL PEAK  2(1P22.1) WILD-TYPE           2       6        2        4        4
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  2(1P22.1) MUTATED           0         0         2          0
  DEL PEAK  2(1P22.1) WILD-TYPE         3         2         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  2(1P22.1) MUTATED            3          6        0
  DEL PEAK  2(1P22.1) WILD-TYPE          4          3        3
D16V8, multiclass

Clustering(17) Variable = Del Peak  3(2q37.3) mutation analysis
D17V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q37.3) MUTATED    9  9
  DEL PEAK  3(2Q37.3) WILD-TYPE 23 25
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           18                            48 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            9                            25 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 TCGA-DA-A1I0 TCGA-EE-A20B 
       11.87        12.10        58.03       148.31        20.38       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A2MH 
       78.87       168.26        47.84        39.62        56.42        16.96 
TCGA-EE-A2MK TCGA-EE-A3AF TCGA-EE-A3AG TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZM 
      144.76        13.81        23.47        48.59       228.59       101.26 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE 
      112.54        71.80       121.22        31.59        23.77        60.23 
TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30         6.38        36.03       117.17       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
      107.34        61.18        53.92       215.44        15.68        26.86 
TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       63.32        32.19        44.35       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
      135.91       182.01        55.59        19.56        21.67       129.24 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AB 
       28.80        19.76       103.27       103.17       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
        3.68       138.77         6.41         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71        11.41       148.77       120.46        84.72 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        11.87                          3.68 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       228.59                        357.37 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       52.505                        57.170 
[1] "11.9 - 228.6 (52.5)" "3.7 - 357.4 (57.2)" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  3(2Q37.3) MUTATED" "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-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  3(2Q37.3) MUTATED" "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-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  3(2Q37.3) MUTATED" "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-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
[1] "hr=" "1.1"
D17V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  3(2Q37.3) MUTATED                    2             0
  DEL PEAK  3(2Q37.3) WILD-TYPE                  4             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  3(2Q37.3) MUTATED                                                                                          5
  DEL PEAK  3(2Q37.3) WILD-TYPE                                                                                        7
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  3(2Q37.3) MUTATED                    11
  DEL PEAK  3(2Q37.3) WILD-TYPE                  37
D17V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  3(2Q37.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                               11
                                                                                          clus
vv                                                                                         DEL PEAK  3(2Q37.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   4
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             7
  REGIONAL LYMPH NODE                                                                                                 37
D17V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      7   11
  DEL PEAK  3(2Q37.3) WILD-TYPE   15   34
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                           7                            15
  MALE                            11                            34
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  3(2Q37.3) MUTATED   14  0   1   1   0
  DEL PEAK  3(2Q37.3) WILD-TYPE 42  1   0   0   2
D17V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  3(2Q37.3) MUTATED   10  0   0   2   0   1   1  2  0
  DEL PEAK  3(2Q37.3) WILD-TYPE 23  1   2   5   1   4   2  5  2
D17V6, multiclass
D17V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  3(2Q37.3) MUTATED             0       2        0        2        4
  DEL PEAK  3(2Q37.3) WILD-TYPE           2       8        2        3        4
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  3(2Q37.3) MUTATED           1         1         1          0
  DEL PEAK  3(2Q37.3) WILD-TYPE         2         1         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED            1          3        0
  DEL PEAK  3(2Q37.3) WILD-TYPE          6          6        3
D17V8, multiclass

Clustering(18) Variable = Del Peak  4(3p26.1) mutation analysis
D18V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(3P26.1) MUTATED    8  8
  DEL PEAK  4(3P26.1) WILD-TYPE 24 26
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                           16                            50 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                            8                            26 
$`DEL PEAK  4(3P26.1) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 
      112.54       121.22        31.59        58.03        36.03       176.55 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2M6 TCGA-EE-A2M7 
      107.34        61.18        78.87        56.42       129.24        28.80 
TCGA-EE-A2M8 TCGA-FS-A1YX TCGA-FS-A1ZM TCGA-GN-A262 
       19.76        48.59       101.26       120.46 

$`DEL PEAK  4(3P26.1) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO 
       71.80        23.77        11.87        12.10        60.23         9.30 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 
      148.31         6.38       117.17        20.38        35.93        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
      215.44        15.68        26.86       109.64       168.26        63.32 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
       47.84        39.62        32.19        44.35       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB 
      103.27       103.17        16.96       144.76       248.61       122.73 
TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY 
        3.68        13.81        23.47       138.77         6.41       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR 
        7.76       357.37        53.52        15.45        32.71        11.41 
TCGA-FS-A1ZS TCGA-GN-A265 
      148.77        84.72 

  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                        19.76                          3.68 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                       176.55                        357.37 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                       70.025                        50.680 
[1] "19.8 - 176.6 (70.0)" "3.7 - 357.4 (50.7)" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  4(3P26.1) MUTATED"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  4(3P26.1) WILD-TYPE"   "DEL PEAK  4(3P26.1) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  4(3P26.1) WILD-TYPE" "DEL PEAK  4(3P26.1) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  4(3P26.1) MUTATED" "DEL PEAK  4(3P26.1) WILD-TYPE" 
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  4(3P26.1) MUTATED                    1             0
  DEL PEAK  4(3P26.1) WILD-TYPE                  5             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  4(3P26.1) MUTATED                                                                                          4
  DEL PEAK  4(3P26.1) WILD-TYPE                                                                                        8
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  4(3P26.1) MUTATED                    11
  DEL PEAK  4(3P26.1) WILD-TYPE                  37
D18V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  4(3P26.1) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                               11
                                                                                          clus
vv                                                                                         DEL PEAK  4(3P26.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                   5
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             8
  REGIONAL LYMPH NODE                                                                                                 37
D18V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.1) MUTATED      8    8
  DEL PEAK  4(3P26.1) WILD-TYPE   14   37
        clus
vv       DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE
  FEMALE                           8                            14
  MALE                             8                            37
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  4(3P26.1) MUTATED   14  0   0   0   1
  DEL PEAK  4(3P26.1) WILD-TYPE 42  1   1   1   1
D18V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  4(3P26.1) MUTATED    9  1   0   1   1   2   1  0  0
  DEL PEAK  4(3P26.1) WILD-TYPE 24  0   2   6   0   3   2  7  2
D18V6, multiclass
D18V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  4(3P26.1) MUTATED             1       2        0        2        2
  DEL PEAK  4(3P26.1) WILD-TYPE           1       8        2        3        6
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  4(3P26.1) MUTATED           0         1         2          0
  DEL PEAK  4(3P26.1) WILD-TYPE         3         1         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  4(3P26.1) MUTATED            3          1        1
  DEL PEAK  4(3P26.1) WILD-TYPE          4          8        2
D18V8, multiclass

Clustering(19) Variable = Del Peak  5(3q27.2) mutation analysis
D19V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(3Q27.2) MUTATED    8  5
  DEL PEAK  5(3Q27.2) WILD-TYPE 24 29
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                           13                            53 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                            5                            29 
$`DEL PEAK  5(3Q27.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
      112.54       121.22        36.03       176.55       107.34        61.18 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GS TCGA-EE-A2M8 TCGA-FS-A1YX TCGA-FS-A1ZM 
       32.19        56.42        55.59        19.76        48.59       101.26 
TCGA-GN-A262 
      120.46 

$`DEL PEAK  5(3Q27.2) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80        31.59        23.77        11.87        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       60.23         9.30       148.31         6.38       117.17        20.38 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       35.93        53.92       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M 
       78.87       168.26        63.32        47.84        39.62        44.35 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT 
      345.96        58.75        47.54       135.91       182.01        19.56 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
       21.67       129.24        28.80       103.27       103.17        16.96 
TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      144.76       248.61       122.73         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      138.77         6.41       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       15.45        32.71        11.41       148.77        84.72 

  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                        19.76                          3.68 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                       176.55                        357.37 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                        61.18                         53.52 
[1] "19.8 - 176.6 (61.2)" "3.7 - 357.4 (53.5)" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  5(3Q27.2) WILD-TYPE"   "DEL PEAK  5(3Q27.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  5(3Q27.2) WILD-TYPE" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  5(3Q27.2) MUTATED" "DEL PEAK  5(3Q27.2) WILD-TYPE" 
[1] "hr=" "1.6"
D19V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  5(3Q27.2) MUTATED                    1             0
  DEL PEAK  5(3Q27.2) WILD-TYPE                  5             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  5(3Q27.2) MUTATED                                                                                          4
  DEL PEAK  5(3Q27.2) WILD-TYPE                                                                                        8
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  5(3Q27.2) MUTATED                     8
  DEL PEAK  5(3Q27.2) WILD-TYPE                  40
D19V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  5(3Q27.2) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                8
                                                                                          clus
vv                                                                                         DEL PEAK  5(3Q27.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   5
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             8
  REGIONAL LYMPH NODE                                                                                                 40
D19V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3Q27.2) MUTATED      9    4
  DEL PEAK  5(3Q27.2) WILD-TYPE   13   41
        clus
vv       DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE
  FEMALE                           9                            13
  MALE                             4                            41
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  5(3Q27.2) MUTATED   11  0   0   0   1
  DEL PEAK  5(3Q27.2) WILD-TYPE 45  1   1   1   1
D19V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  5(3Q27.2) MUTATED    7  1   0   1   0   2   1  0  0
  DEL PEAK  5(3Q27.2) WILD-TYPE 26  0   2   6   1   3   2  7  2
D19V6, multiclass
D19V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  5(3Q27.2) MUTATED             1       1        1        2        0
  DEL PEAK  5(3Q27.2) WILD-TYPE           1       9        1        3        8
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  5(3Q27.2) MUTATED           0         1         2          0
  DEL PEAK  5(3Q27.2) WILD-TYPE         3         1         3          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  5(3Q27.2) MUTATED            2          1        1
  DEL PEAK  5(3Q27.2) WILD-TYPE          5          8        2
D19V8, multiclass

Clustering(20) Variable = Del Peak  6(4p16.3) mutation analysis
D20V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4P16.3) MUTATED   11  4
  DEL PEAK  6(4P16.3) WILD-TYPE 21 30
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           15                            51 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                            4                            30 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F 
        9.30       148.31        36.03        15.68       109.64        78.87 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AB 
       47.84        32.19        44.35        21.67       129.24       122.73 
TCGA-EE-A3AG TCGA-FS-A1ZR TCGA-GN-A262 
       23.47        11.41       120.46 

$`DEL PEAK  6(4P16.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       12.10        58.03        60.23         6.38       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T 
       26.86       168.26        63.32        39.62        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT 
       58.75        47.54       135.91       182.01        55.59        19.56 
TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
       28.80        19.76       103.27       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      248.61         3.68        13.81       138.77         6.41        48.59 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-GN-A265 
      101.26       148.77        84.72 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         9.30                          3.68 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       148.31                        357.37 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                        44.35                         58.03 
[1] "9.3 - 148.3 (44.4)" "3.7 - 357.4 (58.0)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  6(4P16.3) WILD-TYPE" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
[1] "hr=" "1.7"
D20V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  6(4P16.3) MUTATED                    0             1
  DEL PEAK  6(4P16.3) WILD-TYPE                  6             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  6(4P16.3) MUTATED                                                                                          5
  DEL PEAK  6(4P16.3) WILD-TYPE                                                                                        7
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  6(4P16.3) MUTATED                     9
  DEL PEAK  6(4P16.3) WILD-TYPE                  39
D20V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  6(4P16.3) MUTATED
  DISTANT METASTASIS                                                                                                 0
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                                9
                                                                                          clus
vv                                                                                         DEL PEAK  6(4P16.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   6
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             7
  REGIONAL LYMPH NODE                                                                                                 39
D20V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4P16.3) MUTATED      5   10
  DEL PEAK  6(4P16.3) WILD-TYPE   17   35
        clus
vv       DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE
  FEMALE                           5                            17
  MALE                            10                            35
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  6(4P16.3) MUTATED   11  0   0   1   0
  DEL PEAK  6(4P16.3) WILD-TYPE 45  1   1   0   2
D20V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  6(4P16.3) MUTATED    8  0   0   1   0   1   1  1  0
  DEL PEAK  6(4P16.3) WILD-TYPE 25  1   2   6   1   4   2  6  2
D20V6, multiclass
D20V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  6(4P16.3) MUTATED             0       2        1        2        3
  DEL PEAK  6(4P16.3) WILD-TYPE           2       8        1        3        5
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  6(4P16.3) MUTATED           0         0         1          0
  DEL PEAK  6(4P16.3) WILD-TYPE         3         2         4          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  6(4P16.3) MUTATED            2          0        0
  DEL PEAK  6(4P16.3) WILD-TYPE          5          9        3
D20V8, multiclass

Clustering(21) Variable = Del Peak  7(4q34.3) mutation analysis
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(4Q34.3) MUTATED   12  6
  DEL PEAK  7(4Q34.3) WILD-TYPE 20 28
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           18                            48 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            6                            28 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-D3-A2JD TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 
       11.87       148.31        36.03       117.17        61.18       215.44 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T 
       15.68       109.64       168.26        47.84        44.35       345.96 
TCGA-EE-A2A6 TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A3AG TCGA-FS-A1ZC TCGA-FS-A1ZF 
       58.75        21.67       129.24        23.47       357.37        15.45 

$`DEL PEAK  7(4Q34.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JK 
      112.54        71.80       121.22        31.59        23.77        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A1I2 
       58.03        60.23         9.30         6.38        20.38       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A 
       35.93       107.34        53.92        26.86        78.87        63.32 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH 
       39.62        32.19        56.42        47.54       135.91       182.01 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       55.59        19.56        28.80        19.76       103.27       103.17 
TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF 
       16.96       144.76       248.61       122.73         3.68        13.81 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZD 
      138.77         6.41        48.59       228.59         7.76        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71       101.26        11.41       148.77       120.46        84.72 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        11.87                          3.68 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       357.37                        248.61 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                       59.965                        54.755 
[1] "11.9 - 357.4 (60.0)" "3.7 - 248.6 (54.8)" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK  7(4Q34.3) MUTATED"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  7(4Q34.3) MUTATED" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  7(4Q34.3) WILD-TYPE"   "DEL PEAK  7(4Q34.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK  7(4Q34.3) WILD-TYPE" "DEL PEAK  7(4Q34.3) WILD-TYPE" 
[1] "hr=" "2.6"
D21V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  7(4Q34.3) MUTATED                    3             1
  DEL PEAK  7(4Q34.3) WILD-TYPE                  3             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  7(4Q34.3) MUTATED                                                                                          3
  DEL PEAK  7(4Q34.3) WILD-TYPE                                                                                        9
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  7(4Q34.3) MUTATED                    11
  DEL PEAK  7(4Q34.3) WILD-TYPE                  37
D21V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  7(4Q34.3) MUTATED
  DISTANT METASTASIS                                                                                                 3
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           3
  REGIONAL LYMPH NODE                                                                                               11
                                                                                          clus
vv                                                                                         DEL PEAK  7(4Q34.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   3
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             9
  REGIONAL LYMPH NODE                                                                                                 37
D21V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(4Q34.3) MUTATED      5   13
  DEL PEAK  7(4Q34.3) WILD-TYPE   17   32
        clus
vv       DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE
  FEMALE                           5                            17
  MALE                            13                            32
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  7(4Q34.3) MUTATED   16  0   0   1   0
  DEL PEAK  7(4Q34.3) WILD-TYPE 40  1   1   0   2
D21V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  7(4Q34.3) MUTATED    9  0   0   2   0   2   0  3  1
  DEL PEAK  7(4Q34.3) WILD-TYPE 24  1   2   5   1   3   3  4  1
D21V6, multiclass
D21V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  7(4Q34.3) MUTATED             1       3        1        2        1
  DEL PEAK  7(4Q34.3) WILD-TYPE           1       7        1        3        7
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  7(4Q34.3) MUTATED           0         1         0          0
  DEL PEAK  7(4Q34.3) WILD-TYPE         3         1         5          2
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  7(4Q34.3) MUTATED            3          3        0
  DEL PEAK  7(4Q34.3) WILD-TYPE          4          6        3
D21V8, multiclass

Clustering(22) Variable = Del Peak  8(5q11.2) mutation analysis
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(5Q11.2) MUTATED   15  9
  DEL PEAK  8(5Q11.2) WILD-TYPE 17 25
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           24                            42 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                            9                            25 
$`DEL PEAK  8(5Q11.2) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX 
       31.59        11.87        12.10        58.03       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H 
       36.03        20.38       107.34        61.18       215.44       168.26 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GE 
       47.84        39.62        44.35        56.42        47.54       135.91 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1YX TCGA-GN-A262 
      248.61       122.73         3.68       138.77        48.59       120.46 

$`DEL PEAK  8(5Q11.2) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-D3-A3MO 
      112.54        71.80       121.22        23.77        60.23         9.30 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
      117.17       176.55        35.93        53.92        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2A6 
      109.64        78.87        63.32        32.19       345.96        58.75 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
      182.01        55.59        19.56        21.67       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AF 
       19.76       103.27       103.17        16.96       144.76        13.81 
TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
       23.47         6.41       228.59         7.76       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       15.45        32.71       101.26        11.41       148.77        84.72 

  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                         3.68                          6.41 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                       248.61                        357.37 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                       52.505                        57.170 
[1] "3.7 - 248.6 (52.5)" "6.4 - 357.4 (57.2)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  8(5Q11.2) WILD-TYPE"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  8(5Q11.2) MUTATED"   "DEL PEAK  8(5Q11.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  8(5Q11.2) WILD-TYPE" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  8(5Q11.2) MUTATED" "DEL PEAK  8(5Q11.2) WILD-TYPE" 
[1] "hr=" "1.5"
D22V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  8(5Q11.2) MUTATED                    2             1
  DEL PEAK  8(5Q11.2) WILD-TYPE                  4             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  8(5Q11.2) MUTATED                                                                                          4
  DEL PEAK  8(5Q11.2) WILD-TYPE                                                                                        8
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  8(5Q11.2) MUTATED                    17
  DEL PEAK  8(5Q11.2) WILD-TYPE                  31
D22V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  8(5Q11.2) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                               17
                                                                                          clus
vv                                                                                         DEL PEAK  8(5Q11.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   4
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             8
  REGIONAL LYMPH NODE                                                                                                 31
D22V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q11.2) MUTATED      9   15
  DEL PEAK  8(5Q11.2) WILD-TYPE   13   30
        clus
vv       DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE
  FEMALE                           9                            13
  MALE                            15                            30
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  8(5Q11.2) MUTATED   18  0   1   1   1
  DEL PEAK  8(5Q11.2) WILD-TYPE 38  1   0   0   1
D22V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  8(5Q11.2) MUTATED   10  0   1   3   1   2   0  3  1
  DEL PEAK  8(5Q11.2) WILD-TYPE 23  1   1   4   0   3   3  4  1
D22V6, multiclass
D22V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  8(5Q11.2) MUTATED             0       4        0        3        1
  DEL PEAK  8(5Q11.2) WILD-TYPE           2       6        2        2        7
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  8(5Q11.2) MUTATED           0         1         0          1
  DEL PEAK  8(5Q11.2) WILD-TYPE         3         1         5          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  8(5Q11.2) MUTATED            4          4        1
  DEL PEAK  8(5Q11.2) WILD-TYPE          3          5        2
D22V8, multiclass

Clustering(23) Variable = Del Peak  9(5q31.3) mutation analysis
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q31.3) MUTATED   19 13
  DEL PEAK  9(5Q31.3) WILD-TYPE 13 21
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           32                            34 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           13                            21 
$`DEL PEAK  9(5Q31.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D9-A148 TCGA-D9-A1JX 
       31.59        11.87        12.10        58.03       148.31         6.38 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       36.03       117.17        20.38       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
      215.44       168.26        47.84        39.62        44.35        56.42 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MP 
       47.54       135.91        19.56       129.24       103.17       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1ZC TCGA-FS-A1ZF 
      122.73         3.68       138.77        48.59       357.37        15.45 
TCGA-FS-A1ZM TCGA-GN-A262 
      101.26       120.46 

$`DEL PEAK  9(5Q31.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-D3-A3MO 
      112.54        71.80       121.22        23.77        60.23         9.30 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
      176.55        35.93        15.68        26.86       109.64        78.87 
TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GS 
       63.32        32.19       345.96        58.75       182.01        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MK 
       21.67        28.80        19.76       103.27        16.96       144.76 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZD 
       13.81        23.47         6.41       228.59         7.76        53.52 
TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       32.71        11.41       148.77        84.72 

  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                         3.68                          6.41 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                       357.37                        345.96 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                       57.225                        54.555 
[1] "3.7 - 357.4 (57.2)" "6.4 - 346.0 (54.6)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK  9(5Q31.3) MUTATED"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
"DEL PEAK  9(5Q31.3) WILD-TYPE"   "DEL PEAK  9(5Q31.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
"DEL PEAK  9(5Q31.3) WILD-TYPE" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  9(5Q31.3) MUTATED" "DEL PEAK  9(5Q31.3) WILD-TYPE" 
[1] "hr=" "1.8"
D23V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  9(5Q31.3) MUTATED                    4             1
  DEL PEAK  9(5Q31.3) WILD-TYPE                  2             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  9(5Q31.3) MUTATED                                                                                          6
  DEL PEAK  9(5Q31.3) WILD-TYPE                                                                                        6
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  9(5Q31.3) MUTATED                    21
  DEL PEAK  9(5Q31.3) WILD-TYPE                  27
D23V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  9(5Q31.3) MUTATED
  DISTANT METASTASIS                                                                                                 4
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           6
  REGIONAL LYMPH NODE                                                                                               21
                                                                                          clus
vv                                                                                         DEL PEAK  9(5Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   2
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             6
  REGIONAL LYMPH NODE                                                                                                 27
D23V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q31.3) MUTATED     11   21
  DEL PEAK  9(5Q31.3) WILD-TYPE   11   24
        clus
vv       DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE
  FEMALE                          11                            11
  MALE                            21                            24
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK  9(5Q31.3) MUTATED   26  0   1   1   1
  DEL PEAK  9(5Q31.3) WILD-TYPE 30  1   0   0   1
D23V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  9(5Q31.3) MUTATED   15  0   1   3   1   2   1  5  1
  DEL PEAK  9(5Q31.3) WILD-TYPE 18  1   1   4   0   3   2  2  1
D23V6, multiclass
D23V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK  9(5Q31.3) MUTATED             1       6        0        3        1
  DEL PEAK  9(5Q31.3) WILD-TYPE           1       4        2        2        7
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK  9(5Q31.3) MUTATED           1         2         1          1
  DEL PEAK  9(5Q31.3) WILD-TYPE         2         0         4          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  9(5Q31.3) MUTATED            4          6        1
  DEL PEAK  9(5Q31.3) WILD-TYPE          3          3        2
D23V8, multiclass

Clustering(24) Variable = Del Peak 10(6q25.2) mutation analysis
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(6Q25.2) MUTATED   23 21
  DEL PEAK 10(6Q25.2) WILD-TYPE  9 13
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           44                            22 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           21                            13 
$`DEL PEAK 10(6Q25.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 
      112.54        31.59        11.87        58.03        60.23       148.31 
TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
        6.38       117.17        35.93        61.18        53.92       215.44 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       26.86       109.64        78.87       168.26        63.32        47.84 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       32.19        44.35       345.96        58.75        47.54       135.91 
TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK 
       55.59        21.67       129.24        28.80        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J 
      248.61       122.73         3.68        13.81        23.47         6.41 
TCGA-FS-A1YX TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       48.59       357.37        53.52        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS 
       11.41       148.77 

$`DEL PEAK 10(6Q25.2) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3MO TCGA-DA-A1HW 
       71.80       121.22        23.77        12.10         9.30        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A29E TCGA-EE-A29P 
       20.38       176.55       107.34        15.68        39.62        56.42 
TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AH 
      182.01        19.56        19.76       103.27       103.17       138.77 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-GN-A262 TCGA-GN-A265 
      228.59         7.76       120.46        84.72 

  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                         3.68                          7.76 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                       357.37                        228.59 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                       54.755                        64.110 
[1] "3.7 - 357.4 (54.8)" "7.8 - 228.6 (64.1)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 10(6Q25.2) MUTATED" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 10(6Q25.2) WILD-TYPE"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 10(6Q25.2) MUTATED"   "DEL PEAK 10(6Q25.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 10(6Q25.2) WILD-TYPE" "DEL PEAK 10(6Q25.2) WILD-TYPE" 
[1] "hr=" "1.3"
D24V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 10(6Q25.2) MUTATED                    4             1
  DEL PEAK 10(6Q25.2) WILD-TYPE                  2             0
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 10(6Q25.2) MUTATED                                                                                          8
  DEL PEAK 10(6Q25.2) WILD-TYPE                                                                                        4
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 10(6Q25.2) MUTATED                    32
  DEL PEAK 10(6Q25.2) WILD-TYPE                  16
D24V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 10(6Q25.2) MUTATED
  DISTANT METASTASIS                                                                                                 4
  PRIMARY TUMOR                                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           8
  REGIONAL LYMPH NODE                                                                                               32
                                                                                          clus
vv                                                                                         DEL PEAK 10(6Q25.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   2
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             4
  REGIONAL LYMPH NODE                                                                                                 16
D24V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6Q25.2) MUTATED     15   30
  DEL PEAK 10(6Q25.2) WILD-TYPE    7   15
        clus
vv       DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE
  FEMALE                          15                             7
  MALE                            30                            15
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK 10(6Q25.2) MUTATED   38  1   0   1   1
  DEL PEAK 10(6Q25.2) WILD-TYPE 18  0   1   0   1
D24V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 10(6Q25.2) MUTATED   24  0   2   3   1   2   2  5  2
  DEL PEAK 10(6Q25.2) WILD-TYPE  9  1   0   4   0   3   1  2  0
D24V6, multiclass
D24V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 10(6Q25.2) MUTATED             2       7        2        4        7
  DEL PEAK 10(6Q25.2) WILD-TYPE           0       3        0        1        1
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 10(6Q25.2) MUTATED           1         1         2          2
  DEL PEAK 10(6Q25.2) WILD-TYPE         2         1         3          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 10(6Q25.2) MUTATED            4          4        2
  DEL PEAK 10(6Q25.2) WILD-TYPE          3          5        1
D24V8, multiclass

Clustering(25) Variable = Del Peak 11(6q27) mutation analysis
D25V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 11(6Q27) MUTATED   22 21
  DEL PEAK 11(6Q27) WILD-TYPE 10 13
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         43                          23 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         21                          13 
$`DEL PEAK 11(6Q27) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D9-A148 
      112.54        31.59        11.87        58.03        60.23       148.31 
TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
        6.38       117.17        35.93        61.18        53.92       215.44 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
       26.86       109.64       168.26        63.32        47.84        32.19 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS 
       44.35       345.96        58.75        47.54       135.91        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       21.67       129.24        28.80        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1YX 
      122.73         3.68        13.81        23.47         6.41        48.59 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
      357.37        53.52        15.45        32.71       101.26        11.41 
TCGA-FS-A1ZS 
      148.77 

$`DEL PEAK 11(6Q27) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3MO TCGA-DA-A1HW 
       71.80       121.22        23.77        12.10         9.30        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A29E 
       20.38       176.55       107.34        15.68        78.87        39.62 
TCGA-EE-A29P TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       56.42       182.01        19.56        19.76       103.27       103.17 
TCGA-EE-A3AH TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-GN-A262 TCGA-GN-A265 
      138.77       228.59         7.76       120.46        84.72 

  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                       3.68                        7.76 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                     357.37                      228.59 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                      53.92                       71.80 
[1] "3.7 - 357.4 (53.9)" "7.8 - 228.6 (71.8)"
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D3-A1Q5                  TCGA-D3-A1Q6 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D3-A1Q7                  TCGA-D3-A1Q9 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2J9                  TCGA-D3-A2JD 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A2JK                  TCGA-D3-A3C6 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-D3-A3CE                  TCGA-D3-A3MO 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-D9-A148                  TCGA-D9-A1JX 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1HW                  TCGA-DA-A1HY 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A1I0                  TCGA-DA-A1I2 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I4                  TCGA-DA-A1I5 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-DA-A1I7                  TCGA-DA-A1I8 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-DA-A3F5                  TCGA-DA-A3F8 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A183                  TCGA-EE-A20B 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A20F                  TCGA-EE-A20H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29A                  TCGA-EE-A29C 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29E                  TCGA-EE-A29H 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A29M                  TCGA-EE-A29P 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A29T                  TCGA-EE-A2A6 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GB                  TCGA-EE-A2GE 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GH                  TCGA-EE-A2GS 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2GT                  TCGA-EE-A2M5 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M6                  TCGA-EE-A2M7 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2M8                  TCGA-EE-A2ME 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-EE-A2MG                  TCGA-EE-A2MH 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A2MK                  TCGA-EE-A2MP 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AB                  TCGA-EE-A3AD 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AF                  TCGA-EE-A3AG 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-EE-A3AH                  TCGA-ER-A19J 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1YX                  TCGA-FS-A1YY 
  "DEL PEAK 11(6Q27) MUTATED" "DEL PEAK 11(6Q27) WILD-TYPE" 
                 TCGA-FS-A1Z7                  TCGA-FS-A1ZC 
"DEL PEAK 11(6Q27) WILD-TYPE"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZD                  TCGA-FS-A1ZF 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZH                  TCGA-FS-A1ZM 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-FS-A1ZR                  TCGA-FS-A1ZS 
  "DEL PEAK 11(6Q27) MUTATED"   "DEL PEAK 11(6Q27) MUTATED" 
                 TCGA-GN-A262                  TCGA-GN-A265 
"DEL PEAK 11(6Q27) WILD-TYPE" "DEL PEAK 11(6Q27) WILD-TYPE" 
[1] "hr=" "1.2"
D25V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 11(6Q27) MUTATED                    4             1
  DEL PEAK 11(6Q27) WILD-TYPE                  2             0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 11(6Q27) MUTATED                                                                                          8
  DEL PEAK 11(6Q27) WILD-TYPE                                                                                        4
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 11(6Q27) MUTATED                    31
  DEL PEAK 11(6Q27) WILD-TYPE                  17
D25V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 11(6Q27) MUTATED
  DISTANT METASTASIS                                                                                               4
  PRIMARY TUMOR                                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         8
  REGIONAL LYMPH NODE                                                                                             31
                                                                                          clus
vv                                                                                         DEL PEAK 11(6Q27) WILD-TYPE
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                               17
D25V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q27) MUTATED     15   29
  DEL PEAK 11(6Q27) WILD-TYPE    7   16
        clus
vv       DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
  FEMALE                        15                           7
  MALE                          29                          16
                             vv
clus                          M0 M1 M1A M1B M1C
  DEL PEAK 11(6Q27) MUTATED   37  1   0   1   1
  DEL PEAK 11(6Q27) WILD-TYPE 19  0   1   0   1
D25V5, multiclass
                             vv
clus                          N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 11(6Q27) MUTATED   23  0   2   3   1   2   2  5  2
  DEL PEAK 11(6Q27) WILD-TYPE 10  1   0   4   0   3   1  2  0
D25V6, multiclass
D25V7, continuous
                             vv
clus                          I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 11(6Q27) MUTATED             2       7        2        4        6
  DEL PEAK 11(6Q27) WILD-TYPE           0       3        0        1        2
                             vv
clus                          STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 11(6Q27) MUTATED           1         1         2          2
  DEL PEAK 11(6Q27) WILD-TYPE         2         1         3          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(6Q27) MUTATED            4          4        2
  DEL PEAK 11(6Q27) WILD-TYPE          3          5        1
D25V8, multiclass

Clustering(26) Variable = Del Peak 12(9p21.3) mutation analysis
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(9P21.3) MUTATED   27 26
  DEL PEAK 12(9P21.3) WILD-TYPE  5  8
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           53                            13 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           26                             8 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO 
      112.54        71.80        12.10        58.03        60.23         9.30 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
      148.31         6.38        36.03       117.17       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20F 
      107.34        61.18        53.92       215.44       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P 
      168.26        63.32        47.84        39.62        32.19        56.42 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS 
      345.96        58.75        47.54       135.91       182.01        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       21.67       129.24        19.76        16.96       144.76       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
      122.73         3.68        13.81        23.47       138.77         6.41 
TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
       48.59       228.59         7.76       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       32.71       101.26        11.41       148.77        84.72 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-DA-A1I0 TCGA-DA-A3F8 
      121.22        31.59        23.77        11.87        20.38        15.68 
TCGA-EE-A183 TCGA-EE-A29M TCGA-EE-A2GT TCGA-EE-A2M7 TCGA-EE-A2ME TCGA-EE-A2MG 
       26.86        44.35        19.56        28.80       103.27       103.17 
TCGA-GN-A262 
      120.46 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         3.68                         11.87 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                       357.37                        121.22 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        58.75                         28.80 
[1] "3.7 - 357.4 (58.8)"  "11.9 - 121.2 (28.8)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 12(9P21.3) WILD-TYPE" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 12(9P21.3) MUTATED" "DEL PEAK 12(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 12(9P21.3) MUTATED"   "DEL PEAK 12(9P21.3) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"DEL PEAK 12(9P21.3) WILD-TYPE"   "DEL PEAK 12(9P21.3) MUTATED" 
[1] "hr=" "2"  
D26V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 12(9P21.3) MUTATED                    6             0
  DEL PEAK 12(9P21.3) WILD-TYPE                  0             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 12(9P21.3) MUTATED                                                                                         10
  DEL PEAK 12(9P21.3) WILD-TYPE                                                                                        2
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 12(9P21.3) MUTATED                    38
  DEL PEAK 12(9P21.3) WILD-TYPE                  10
D26V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 12(9P21.3) MUTATED
  DISTANT METASTASIS                                                                                                 6
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          10
  REGIONAL LYMPH NODE                                                                                               38
                                                                                          clus
vv                                                                                         DEL PEAK 12(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   0
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
  REGIONAL LYMPH NODE                                                                                                 10
D26V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     19   35
  DEL PEAK 12(9P21.3) WILD-TYPE    3   10
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          19                             3
  MALE                            35                            10
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK 12(9P21.3) MUTATED   45  1   0   1   2
  DEL PEAK 12(9P21.3) WILD-TYPE 11  0   1   0   0
D26V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 12(9P21.3) MUTATED   26  1   2   6   0   4   3  5  2
  DEL PEAK 12(9P21.3) WILD-TYPE  7  0   0   1   1   1   0  2  0
D26V6, multiclass
D26V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 12(9P21.3) MUTATED             2       7        2        3        7
  DEL PEAK 12(9P21.3) WILD-TYPE           0       3        0        2        1
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 12(9P21.3) MUTATED           2         2         5          2
  DEL PEAK 12(9P21.3) WILD-TYPE         1         0         0          0
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(9P21.3) MUTATED            5          6        3
  DEL PEAK 12(9P21.3) WILD-TYPE          2          3        0
D26V8, multiclass

Clustering(27) Variable = Del Peak 13(9q21.2) mutation analysis
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(9Q21.2) MUTATED   18 16
  DEL PEAK 13(9Q21.2) WILD-TYPE 14 18
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                           34                            32 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                           16                            18 
$`DEL PEAK 13(9Q21.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 
      112.54        58.03         9.30       148.31        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20F 
       35.93       107.34        53.92       215.44       109.64        78.87 
TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M6 
      168.26        56.42        47.54       135.91        55.59       129.24 
TCGA-EE-A2M8 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF 
       19.76        16.96       144.76       248.61         3.68        13.81 
TCGA-EE-A3AG TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM 
       23.47       228.59       357.37        15.45        32.71       101.26 
TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       11.41       148.77       120.46        84.72 

$`DEL PEAK 13(9Q21.2) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       71.80       121.22        31.59        23.77        11.87        12.10 
TCGA-D3-A3CE TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F8 
       60.23         6.38       117.17        20.38        61.18        15.68 
TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       26.86        63.32        47.84        39.62        32.19        44.35 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 
      345.96        58.75       182.01        19.56        21.67        28.80 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A3AB TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX 
      103.27       103.17       122.73       138.77         6.41        48.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZD 
        7.76        53.52 

  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                         3.68                          6.38 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                       357.37                        345.96 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                       81.795                        46.095 
[1] "3.7 - 357.4 (81.8)" "6.4 - 346.0 (46.1)"
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D3-A1Q5                    TCGA-D3-A1Q6 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A1Q7                    TCGA-D3-A1Q9 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2J9                    TCGA-D3-A2JD 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-D3-A2JK                    TCGA-D3-A3C6 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D3-A3CE                    TCGA-D3-A3MO 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-D9-A148                    TCGA-D9-A1JX 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1HW                    TCGA-DA-A1HY 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-DA-A1I0                    TCGA-DA-A1I2 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I4                    TCGA-DA-A1I5 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A1I7                    TCGA-DA-A1I8 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-DA-A3F5                    TCGA-DA-A3F8 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A183                    TCGA-EE-A20B 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A20F                    TCGA-EE-A20H 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29A                    TCGA-EE-A29C 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29E                    TCGA-EE-A29H 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A29M                    TCGA-EE-A29P 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A29T                    TCGA-EE-A2A6 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2GB                    TCGA-EE-A2GE 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GH                    TCGA-EE-A2GS 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2GT                    TCGA-EE-A2M5 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M6                    TCGA-EE-A2M7 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2M8                    TCGA-EE-A2ME 
  "DEL PEAK 13(9Q21.2) MUTATED" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-EE-A2MG                    TCGA-EE-A2MH 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A2MK                    TCGA-EE-A2MP 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AB                    TCGA-EE-A3AD 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AF                    TCGA-EE-A3AG 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-EE-A3AH                    TCGA-ER-A19J 
"DEL PEAK 13(9Q21.2) WILD-TYPE" "DEL PEAK 13(9Q21.2) WILD-TYPE" 
                   TCGA-FS-A1YX                    TCGA-FS-A1YY 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1Z7                    TCGA-FS-A1ZC 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZD                    TCGA-FS-A1ZF 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZH                    TCGA-FS-A1ZM 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-FS-A1ZR                    TCGA-FS-A1ZS 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK 13(9Q21.2) MUTATED"   "DEL PEAK 13(9Q21.2) MUTATED" 
[1] "hr=" "1.8"
D27V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 13(9Q21.2) MUTATED                    5             0
  DEL PEAK 13(9Q21.2) WILD-TYPE                  1             1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 13(9Q21.2) MUTATED                                                                                          8
  DEL PEAK 13(9Q21.2) WILD-TYPE                                                                                        4
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 13(9Q21.2) MUTATED                    21
  DEL PEAK 13(9Q21.2) WILD-TYPE                  27
D27V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 13(9Q21.2) MUTATED
  DISTANT METASTASIS                                                                                                 5
  PRIMARY TUMOR                                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           8
  REGIONAL LYMPH NODE                                                                                               21
                                                                                          clus
vv                                                                                         DEL PEAK 13(9Q21.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             4
  REGIONAL LYMPH NODE                                                                                                 27
D27V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(9Q21.2) MUTATED     15   19
  DEL PEAK 13(9Q21.2) WILD-TYPE    7   26
        clus
vv       DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE
  FEMALE                          15                             7
  MALE                            19                            26
                               vv
clus                            M0 M1 M1A M1B M1C
  DEL PEAK 13(9Q21.2) MUTATED   26  0   0   1   2
  DEL PEAK 13(9Q21.2) WILD-TYPE 30  1   1   0   0
D27V5, multiclass
                               vv
clus                            N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 13(9Q21.2) MUTATED   18  1   1   1   0   2   3  3  0
  DEL PEAK 13(9Q21.2) WILD-TYPE 15  0   1   6   1   3   0  4  2
D27V6, multiclass
D27V7, continuous
                               vv
clus                            I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 13(9Q21.2) MUTATED             2       4        0        2        6
  DEL PEAK 13(9Q21.2) WILD-TYPE           0       6        2        3        2
                               vv
clus                            STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 13(9Q21.2) MUTATED           1         2         3          1
  DEL PEAK 13(9Q21.2) WILD-TYPE         2         0         2          1
                               vv
clus                            STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 13(9Q21.2) MUTATED            2          3        2
  DEL PEAK 13(9Q21.2) WILD-TYPE          5          6        1
D27V8, multiclass

Clustering(28) Variable = Del Peak 14(10q21.1) mutation analysis
D28V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(10Q21.1) MUTATED   21 27
  DEL PEAK 14(10Q21.1) WILD-TYPE 11  7
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            48                             18 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            27                              7 
$`DEL PEAK 14(10Q21.1) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        31.59        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 
       58.03        60.23         9.30       148.31        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       35.93       107.34        61.18        53.92       215.44        15.68 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
      109.64       168.26        32.19        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2M7 
       58.75        47.54       135.91        55.59       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AD 
       19.76       103.17        16.96       144.76       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
       13.81       138.77        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A262 
       53.52        15.45        32.71       101.26        11.41       120.46 

$`DEL PEAK 14(10Q21.1) WILD-TYPE`
TCGA-D3-A2J9 TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-EE-A183 TCGA-EE-A20F 
       23.77         6.38       117.17        20.38        26.86        78.87 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M5 
       63.32        47.84        39.62       182.01        19.56        21.67 
TCGA-EE-A2ME TCGA-EE-A2MP TCGA-EE-A3AG TCGA-ER-A19J TCGA-FS-A1ZS TCGA-GN-A265 
      103.27       248.61        23.47         6.41       148.77        84.72 

  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                          3.68                           6.38 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                        357.37                         248.61 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                        57.225                         43.730 
[1] "3.7 - 357.4 (57.2)" "6.4 - 248.6 (43.7)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 14(10Q21.1) WILD-TYPE" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 14(10Q21.1) MUTATED"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
[1] "hr=" "1.2"
D28V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 14(10Q21.1) MUTATED                    5             1
  DEL PEAK 14(10Q21.1) WILD-TYPE                  1             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 14(10Q21.1) MUTATED                                                                                         10
  DEL PEAK 14(10Q21.1) WILD-TYPE                                                                                        2
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 14(10Q21.1) MUTATED                    32
  DEL PEAK 14(10Q21.1) WILD-TYPE                  16
D28V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 14(10Q21.1) MUTATED
  DISTANT METASTASIS                                                                                                  5
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           10
  REGIONAL LYMPH NODE                                                                                                32
                                                                                          clus
vv                                                                                         DEL PEAK 14(10Q21.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    1
  PRIMARY TUMOR                                                                                                         0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
  REGIONAL LYMPH NODE                                                                                                  16
D28V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(10Q21.1) MUTATED     20   28
  DEL PEAK 14(10Q21.1) WILD-TYPE    2   17
        clus
vv       DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE
  FEMALE                           20                              2
  MALE                             28                             17
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 14(10Q21.1) MUTATED   41  0   0   1   2
  DEL PEAK 14(10Q21.1) WILD-TYPE 15  1   1   0   0
D28V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 14(10Q21.1) MUTATED   24  1   1   5   1   5   3  3  1
  DEL PEAK 14(10Q21.1) WILD-TYPE  9  0   1   2   0   0   0  4  1
D28V6, multiclass
D28V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 14(10Q21.1) MUTATED             2       5        2        4        6
  DEL PEAK 14(10Q21.1) WILD-TYPE           0       5        0        1        2
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 14(10Q21.1) MUTATED           2         2         5          1
  DEL PEAK 14(10Q21.1) WILD-TYPE         1         0         0          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 14(10Q21.1) MUTATED            5          6        2
  DEL PEAK 14(10Q21.1) WILD-TYPE          2          3        1
D28V8, multiclass

Clustering(29) Variable = Del Peak 15(10q23.31) mutation analysis
D29V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(10Q23.31) MUTATED   25 26
  DEL PEAK 15(10Q23.31) WILD-TYPE  7  8
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             51                              15 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             26                               8 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK 
      112.54        71.80       121.22        31.59        11.87        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       58.03        60.23         9.30       148.31         6.38        36.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
      176.55        35.93       107.34        61.18        53.92       215.44 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M 
       15.68       109.64        78.87       168.26        32.19        44.35 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GS 
       56.42       345.96        58.75        47.54       135.91        55.59 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK 
      129.24        28.80        19.76       103.17        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
      248.61       122.73         3.68        13.81        23.47       138.77 
TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      228.59         7.76       357.37        53.52        15.45        32.71 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-GN-A262 
      101.26        11.41       120.46 

$`DEL PEAK 15(10Q23.31) WILD-TYPE`
TCGA-D3-A2J9 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C 
       23.77       117.17        20.38        26.86        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2ME TCGA-ER-A19J 
       39.62       182.01        19.56        21.67       103.27         6.41 
TCGA-FS-A1YX TCGA-FS-A1ZS TCGA-GN-A265 
       48.59       148.77        84.72 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           3.68                            6.41 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                         357.37                          182.01 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                          58.03                           47.84 
[1] "3.7 - 357.4 (58.0)" "6.4 - 182.0 (47.8)"
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 15(10Q23.31) MUTATED"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.3"
D29V2, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 15(10Q23.31) MUTATED                    5             1
  DEL PEAK 15(10Q23.31) WILD-TYPE                  1             0
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 15(10Q23.31) MUTATED                                                                                         10
  DEL PEAK 15(10Q23.31) WILD-TYPE                                                                                        2
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 15(10Q23.31) MUTATED                    35
  DEL PEAK 15(10Q23.31) WILD-TYPE                  13
D29V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 15(10Q23.31) MUTATED
  DISTANT METASTASIS                                                                                                   5
  PRIMARY TUMOR                                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            10
  REGIONAL LYMPH NODE                                                                                                 35
                                                                                          clus
vv                                                                                         DEL PEAK 15(10Q23.31) WILD-TYPE
  DISTANT METASTASIS                                                                                                     1
  PRIMARY TUMOR                                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               2
  REGIONAL LYMPH NODE                                                                                                   13
D29V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     21   30
  DEL PEAK 15(10Q23.31) WILD-TYPE    1   15
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            21                               1
  MALE                              30                              15
                                 vv
clus                              M0 M1 M1A M1B M1C
  DEL PEAK 15(10Q23.31) MUTATED   43  0   0   1   2
  DEL PEAK 15(10Q23.31) WILD-TYPE 13  1   1   0   0
D29V5, multiclass
                                 vv
clus                              N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 15(10Q23.31) MUTATED   25  1   1   5   1   5   3  3  2
  DEL PEAK 15(10Q23.31) WILD-TYPE  8  0   1   2   0   0   0  4  0
D29V6, multiclass
D29V7, continuous
                                 vv
clus                              I OR II NOS STAGE I STAGE IA STAGE IB
  DEL PEAK 15(10Q23.31) MUTATED             2       5        2        4
  DEL PEAK 15(10Q23.31) WILD-TYPE           0       5        0        1
                                 vv
clus                              STAGE II STAGE IIA STAGE IIC STAGE III
  DEL PEAK 15(10Q23.31) MUTATED          7         2         2         5
  DEL PEAK 15(10Q23.31) WILD-TYPE        1         1         0         0
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 15(10Q23.31) MUTATED            1          5          6        2
  DEL PEAK 15(10Q23.31) WILD-TYPE          1          2          3        1
D29V8, multiclass

Clustering(30) Variable = Del Peak 16(11q22.3) mutation analysis
D30V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(11Q22.3) MUTATED   22 13
  DEL PEAK 16(11Q22.3) WILD-TYPE 10 21
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            35                             31 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            13                             21 
$`DEL PEAK 16(11Q22.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3MO 
      112.54       121.22        31.59        11.87        58.03         9.30 
TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I8 
      148.31         6.38        36.03        20.38       107.34        53.92 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
      215.44       109.64        78.87       168.26        63.32        47.84 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GB TCGA-EE-A2GE 
       32.19        44.35        56.42       345.96        47.54       135.91 
TCGA-EE-A2M6 TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AG TCGA-FS-A1Z7 
      129.24       248.61       122.73         3.68        23.47         7.76 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-GN-A262 TCGA-GN-A265 
       15.45        32.71       101.26       120.46        84.72 

$`DEL PEAK 16(11Q22.3) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I2 
       71.80        23.77        12.10        60.23       117.17       176.55 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2A6 
       35.93        61.18        15.68        26.86        39.62        58.75 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M7 TCGA-EE-A2M8 
      182.01        55.59        19.56        21.67        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AF TCGA-EE-A3AH 
      103.27       103.17        16.96       144.76        13.81       138.77 
TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZR 
        6.41        48.59       228.59       357.37        53.52        11.41 
TCGA-FS-A1ZS 
      148.77 

  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                          3.68                           6.41 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                        345.96                         357.37 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                         58.03                          53.52 
[1] "3.7 - 346.0 (58.0)" "6.4 - 357.4 (53.5)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 16(11Q22.3) MUTATED" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 16(11Q22.3) WILD-TYPE"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 16(11Q22.3) WILD-TYPE" "DEL PEAK 16(11Q22.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 16(11Q22.3) MUTATED"   "DEL PEAK 16(11Q22.3) MUTATED" 
[1] "hr=" "1.8"
D30V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 16(11Q22.3) MUTATED                    4             1
  DEL PEAK 16(11Q22.3) WILD-TYPE                  2             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 16(11Q22.3) MUTATED                                                                                          7
  DEL PEAK 16(11Q22.3) WILD-TYPE                                                                                        5
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 16(11Q22.3) MUTATED                    24
  DEL PEAK 16(11Q22.3) WILD-TYPE                  24
D30V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 16(11Q22.3) MUTATED
  DISTANT METASTASIS                                                                                                  4
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            7
  REGIONAL LYMPH NODE                                                                                                24
                                                                                          clus
vv                                                                                         DEL PEAK 16(11Q22.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  PRIMARY TUMOR                                                                                                         0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              5
  REGIONAL LYMPH NODE                                                                                                  24
D30V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(11Q22.3) MUTATED     15   21
  DEL PEAK 16(11Q22.3) WILD-TYPE    7   24
        clus
vv       DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE
  FEMALE                           15                              7
  MALE                             21                             24
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 16(11Q22.3) MUTATED   27  0   1   1   2
  DEL PEAK 16(11Q22.3) WILD-TYPE 29  1   0   0   0
D30V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 16(11Q22.3) MUTATED   15  0   2   4   1   0   3  4  2
  DEL PEAK 16(11Q22.3) WILD-TYPE 18  1   0   3   0   5   0  3  0
D30V6, multiclass
D30V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 16(11Q22.3) MUTATED             1       4        1        4        2
  DEL PEAK 16(11Q22.3) WILD-TYPE           1       6        1        1        6
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 16(11Q22.3) MUTATED           0         2         2          2
  DEL PEAK 16(11Q22.3) WILD-TYPE         3         0         3          0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 16(11Q22.3) MUTATED            3          5        2
  DEL PEAK 16(11Q22.3) WILD-TYPE          4          4        1
D30V8, multiclass

Clustering(31) Variable = Del Peak 17(12q24.32) mutation analysis
D31V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 17(12Q24.32) MUTATED    6  5
  DEL PEAK 17(12Q24.32) WILD-TYPE 26 29
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                             11                              55 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                              5                              29 
$`DEL PEAK 17(12Q24.32) MUTATED`
TCGA-D3-A3C6 TCGA-D9-A148 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A2MG TCGA-EE-A2MK 
       58.03       148.31       109.64       168.26       103.17       144.76 
TCGA-EE-A2MP TCGA-EE-A3AD TCGA-FS-A1YX TCGA-FS-A1ZH TCGA-FS-A1ZM 
      248.61         3.68        48.59        32.71       101.26 

$`DEL PEAK 17(12Q24.32) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1HY 
       12.10        60.23         9.30         6.38        36.03       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       20.38       176.55        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
      215.44        15.68        26.86        78.87        63.32        47.84 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       39.62        32.19        44.35        56.42       345.96        58.75 
TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       47.54       135.91       182.01        55.59        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A3AB 
      129.24        28.80        19.76       103.27        16.96       122.73 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1Z7 
       13.81        23.47       138.77         6.41       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
      357.37        53.52        15.45        11.41       148.77       120.46 
TCGA-GN-A265 
       84.72 

  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                           3.68                            6.38 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                         248.61                          357.37 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                         103.17                           53.52 
[1] "3.7 - 248.6 (103.2)" "6.4 - 357.4 (53.5)" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A1Q5                      TCGA-D3-A1Q6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A1Q7                      TCGA-D3-A1Q9 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2J9                      TCGA-D3-A2JD 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D3-A2JK                      TCGA-D3-A3C6 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-D3-A3CE                      TCGA-D3-A3MO 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-D9-A148                      TCGA-D9-A1JX 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1HW                      TCGA-DA-A1HY 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I0                      TCGA-DA-A1I2 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I4                      TCGA-DA-A1I5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A1I7                      TCGA-DA-A1I8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-DA-A3F5                      TCGA-DA-A3F8 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A183                      TCGA-EE-A20B 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A20F                      TCGA-EE-A20H 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A29A                      TCGA-EE-A29C 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29E                      TCGA-EE-A29H 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29M                      TCGA-EE-A29P 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A29T                      TCGA-EE-A2A6 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GB                      TCGA-EE-A2GE 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GH                      TCGA-EE-A2GS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2GT                      TCGA-EE-A2M5 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M6                      TCGA-EE-A2M7 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2M8                      TCGA-EE-A2ME 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MG                      TCGA-EE-A2MH 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A2MK                      TCGA-EE-A2MP 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AB                      TCGA-EE-A3AD 
"DEL PEAK 17(12Q24.32) WILD-TYPE"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-EE-A3AF                      TCGA-EE-A3AG 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-EE-A3AH                      TCGA-ER-A19J 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1YX                      TCGA-FS-A1YY 
  "DEL PEAK 17(12Q24.32) MUTATED" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1Z7                      TCGA-FS-A1ZC 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZD                      TCGA-FS-A1ZF 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZH                      TCGA-FS-A1ZM 
  "DEL PEAK 17(12Q24.32) MUTATED"   "DEL PEAK 17(12Q24.32) MUTATED" 
                     TCGA-FS-A1ZR                      TCGA-FS-A1ZS 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A262                      TCGA-GN-A265 
"DEL PEAK 17(12Q24.32) WILD-TYPE" "DEL PEAK 17(12Q24.32) WILD-TYPE" 
[1] "hr=" "1.5"
D31V2, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 17(12Q24.32) MUTATED                    1             0
  DEL PEAK 17(12Q24.32) WILD-TYPE                  5             1
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 17(12Q24.32) MUTATED                                                                                          3
  DEL PEAK 17(12Q24.32) WILD-TYPE                                                                                        9
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK 17(12Q24.32) MUTATED                     7
  DEL PEAK 17(12Q24.32) WILD-TYPE                  41
D31V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 17(12Q24.32) MUTATED
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             3
  REGIONAL LYMPH NODE                                                                                                  7
                                                                                          clus
vv                                                                                         DEL PEAK 17(12Q24.32) WILD-TYPE
  DISTANT METASTASIS                                                                                                     5
  PRIMARY TUMOR                                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               9
  REGIONAL LYMPH NODE                                                                                                   41
D31V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 17(12Q24.32) MUTATED      6    5
  DEL PEAK 17(12Q24.32) WILD-TYPE   16   40
        clus
vv       DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE
  FEMALE                             6                              16
  MALE                               5                              40
                                 vv
clus                              M0 M1 M1A M1B M1C
  DEL PEAK 17(12Q24.32) MUTATED    8  0   0   1   1
  DEL PEAK 17(12Q24.32) WILD-TYPE 48  1   1   0   1
D31V5, multiclass
                                 vv
clus                              N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 17(12Q24.32) MUTATED    7  0   0   0   0   0   2  1  0
  DEL PEAK 17(12Q24.32) WILD-TYPE 26  1   2   7   1   5   1  6  2
D31V6, multiclass
D31V7, continuous
                                 vv
clus                              I OR II NOS STAGE I STAGE IA STAGE IB
  DEL PEAK 17(12Q24.32) MUTATED             0       4        0        1
  DEL PEAK 17(12Q24.32) WILD-TYPE           2       6        2        4
                                 vv
clus                              STAGE II STAGE IIA STAGE IIC STAGE III
  DEL PEAK 17(12Q24.32) MUTATED          2         0         0         1
  DEL PEAK 17(12Q24.32) WILD-TYPE        6         3         2         4
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 17(12Q24.32) MUTATED            0          0          0        1
  DEL PEAK 17(12Q24.32) WILD-TYPE          2          7          9        2
D31V8, multiclass

Clustering(32) Variable = Del Peak 18(14q31.1) mutation analysis
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(14Q31.1) MUTATED   11 12
  DEL PEAK 18(14Q31.1) WILD-TYPE 21 22
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            23                             43 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            12                             22 
$`DEL PEAK 18(14Q31.1) MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A29C 
       60.23       117.17       107.34        53.92       215.44        47.84 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2M6 TCGA-EE-A2M7 
       56.42       345.96        58.75       135.91       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AH TCGA-FS-A1YX 
       19.76       103.17        16.96       144.76       138.77        48.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        7.76       357.37        32.71       101.26        11.41 

$`DEL PEAK 18(14Q31.1) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW 
       12.10        58.03         9.30       148.31         6.38        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A183 
       20.38       176.55        35.93        61.18        15.68        26.86 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H 
      109.64        78.87       168.26        63.32        39.62        32.19 
TCGA-EE-A29M TCGA-EE-A2GB TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 
       44.35        47.54       182.01        55.59        19.56        21.67 
TCGA-EE-A2ME TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      103.27       248.61       122.73         3.68        13.81        23.47 
TCGA-ER-A19J TCGA-FS-A1YY TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZS TCGA-GN-A262 
        6.41       228.59        53.52        15.45       148.77       120.46 
TCGA-GN-A265 
       84.72 

  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                          7.76                           3.68 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                        357.37                         248.61 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                         60.23                          47.54 
[1] "7.8 - 357.4 (60.2)" "3.7 - 248.6 (47.5)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 18(14Q31.1) MUTATED"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
  "DEL PEAK 18(14Q31.1) MUTATED" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
[1] "hr=" "1.3"
D32V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 18(14Q31.1) MUTATED                    2             0
  DEL PEAK 18(14Q31.1) WILD-TYPE                  4             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 18(14Q31.1) MUTATED                                                                                          4
  DEL PEAK 18(14Q31.1) WILD-TYPE                                                                                        8
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 18(14Q31.1) MUTATED                    17
  DEL PEAK 18(14Q31.1) WILD-TYPE                  31
D32V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 18(14Q31.1) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            4
  REGIONAL LYMPH NODE                                                                                                17
                                                                                          clus
vv                                                                                         DEL PEAK 18(14Q31.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              8
  REGIONAL LYMPH NODE                                                                                                  31
D32V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(14Q31.1) MUTATED      9   14
  DEL PEAK 18(14Q31.1) WILD-TYPE   13   31
        clus
vv       DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE
  FEMALE                            9                             13
  MALE                             14                             31
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 18(14Q31.1) MUTATED   21  0   0   0   2
  DEL PEAK 18(14Q31.1) WILD-TYPE 35  1   1   1   0
D32V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 18(14Q31.1) MUTATED   14  1   0   2   0   0   2  3  1
  DEL PEAK 18(14Q31.1) WILD-TYPE 19  0   2   5   1   5   1  4  1
D32V6, multiclass
D32V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 18(14Q31.1) MUTATED             1       4        1        1        5
  DEL PEAK 18(14Q31.1) WILD-TYPE           1       6        1        4        3
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 18(14Q31.1) MUTATED           0         1         3          0
  DEL PEAK 18(14Q31.1) WILD-TYPE         3         1         2          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 18(14Q31.1) MUTATED            0          4        2
  DEL PEAK 18(14Q31.1) WILD-TYPE          7          5        1
D32V8, multiclass

Clustering(33) Variable = Del Peak 19(15q21.1) mutation analysis
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(15Q21.1) MUTATED    5  8
  DEL PEAK 19(15Q21.1) WILD-TYPE 27 26
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                            13                             53 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             8                             26 
$`DEL PEAK 19(15Q21.1) MUTATED`
TCGA-D3-A3C6 TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A29P 
       58.03       148.31        36.03        53.92        26.86        56.42 
TCGA-EE-A2M5 TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-ER-A19J TCGA-FS-A1YX 
       21.67        16.96       144.76       122.73         6.41        48.59 
TCGA-FS-A1ZM 
      101.26 

$`DEL PEAK 19(15Q21.1) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
      112.54        71.80       121.22        31.59        23.77        11.87 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 
       12.10        60.23         9.30         6.38       117.17        20.38 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
      176.55        35.93       107.34        61.18       215.44        15.68 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
      109.64        78.87       168.26        63.32        47.84        39.62 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
       32.19        44.35       345.96        58.75        47.54       135.91 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 
      182.01        55.59        19.56       129.24        28.80        19.76 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG 
      103.27       103.17       248.61         3.68        13.81        23.47 
TCGA-EE-A3AH TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
      138.77       228.59         7.76       357.37        53.52        15.45 
TCGA-FS-A1ZH TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 TCGA-GN-A265 
       32.71        11.41       148.77       120.46        84.72 

  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                          6.41                           3.68 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                        148.31                         357.37 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                         53.92                          58.75 
[1] "6.4 - 148.3 (53.9)" "3.7 - 357.4 (58.8)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
  "DEL PEAK 19(15Q21.1) MUTATED" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 19(15Q21.1) WILD-TYPE"   "DEL PEAK 19(15Q21.1) MUTATED" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 19(15Q21.1) WILD-TYPE" "DEL PEAK 19(15Q21.1) WILD-TYPE" 
[1] "hr=" "1.6"
D33V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 19(15Q21.1) MUTATED                    0             0
  DEL PEAK 19(15Q21.1) WILD-TYPE                  6             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 19(15Q21.1) MUTATED                                                                                          3
  DEL PEAK 19(15Q21.1) WILD-TYPE                                                                                        9
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 19(15Q21.1) MUTATED                    10
  DEL PEAK 19(15Q21.1) WILD-TYPE                  38
D33V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 19(15Q21.1) MUTATED
  DISTANT METASTASIS                                                                                                  0
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                10
                                                                                          clus
vv                                                                                         DEL PEAK 19(15Q21.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    6
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              9
  REGIONAL LYMPH NODE                                                                                                  38
D33V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      6    7
  DEL PEAK 19(15Q21.1) WILD-TYPE   16   38
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  FEMALE                            6                             16
  MALE                              7                             38
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 19(15Q21.1) MUTATED   10  1   0   1   0
  DEL PEAK 19(15Q21.1) WILD-TYPE 46  0   1   0   2
D33V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 19(15Q21.1) MUTATED    7  0   0   1   0   0   1  3  0
  DEL PEAK 19(15Q21.1) WILD-TYPE 26  1   2   6   1   5   2  4  2
D33V6, multiclass
D33V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 19(15Q21.1) MUTATED             0       3        0        1        2
  DEL PEAK 19(15Q21.1) WILD-TYPE           2       7        2        4        6
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 19(15Q21.1) MUTATED           0         1         1          0
  DEL PEAK 19(15Q21.1) WILD-TYPE         3         1         4          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 19(15Q21.1) MUTATED            1          1        1
  DEL PEAK 19(15Q21.1) WILD-TYPE          6          8        2
D33V8, multiclass

Clustering(34) Variable = Del Peak 20(16q23.3) mutation analysis
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(16Q23.3) MUTATED    9  9
  DEL PEAK 20(16Q23.3) WILD-TYPE 23 25
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                            18                             48 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                             9                             25 
$`DEL PEAK 20(16Q23.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A3CE TCGA-D9-A148 TCGA-DA-A1HW TCGA-DA-A1I2 
      112.54       121.22        60.23       148.31        36.03       176.55 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2M5 
       35.93        15.68        32.19        44.35        56.42        21.67 
TCGA-EE-A2MG TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AF TCGA-FS-A1ZF TCGA-GN-A262 
      103.17       144.76       122.73        13.81        15.45       120.46 

$`DEL PEAK 20(16Q23.3) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       71.80        31.59        23.77        11.87        12.10        58.03 
TCGA-D3-A3MO TCGA-D9-A1JX TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.30         6.38       117.17        20.38       107.34        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       53.92       215.44        26.86       109.64        78.87       168.26 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB 
       63.32        47.84        39.62       345.96        58.75        47.54 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M6 TCGA-EE-A2M7 
      135.91       182.01        55.59        19.56       129.24        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MP TCGA-EE-A3AD TCGA-EE-A3AG 
       19.76       103.27        16.96       248.61         3.68        23.47 
TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC 
      138.77         6.41        48.59       228.59         7.76       357.37 
TCGA-FS-A1ZD TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
       53.52        32.71       101.26        11.41       148.77        84.72 

  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                         13.81                           3.68 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                        176.55                         357.37 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                        58.325                         54.755 
[1] "13.8 - 176.6 (58.3)" "3.7 - 357.4 (54.8)" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q23.3) MUTATED"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q23.3) MUTATED"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
  "DEL PEAK 20(16Q23.3) MUTATED"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
"DEL PEAK 20(16Q23.3) WILD-TYPE"   "DEL PEAK 20(16Q23.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 20(16Q23.3) WILD-TYPE" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 20(16Q23.3) MUTATED" "DEL PEAK 20(16Q23.3) WILD-TYPE" 
[1] "hr=" "1"  
D34V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 20(16Q23.3) MUTATED                    1             1
  DEL PEAK 20(16Q23.3) WILD-TYPE                  5             0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 20(16Q23.3) MUTATED                                                                                          2
  DEL PEAK 20(16Q23.3) WILD-TYPE                                                                                       10
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 20(16Q23.3) MUTATED                    15
  DEL PEAK 20(16Q23.3) WILD-TYPE                  33
D34V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 20(16Q23.3) MUTATED
  DISTANT METASTASIS                                                                                                  1
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            2
  REGIONAL LYMPH NODE                                                                                                15
                                                                                          clus
vv                                                                                         DEL PEAK 20(16Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    5
  PRIMARY TUMOR                                                                                                         0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             10
  REGIONAL LYMPH NODE                                                                                                  33
D34V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(16Q23.3) MUTATED     10    9
  DEL PEAK 20(16Q23.3) WILD-TYPE   12   36
        clus
vv       DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE
  FEMALE                           10                             12
  MALE                              9                             36
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 20(16Q23.3) MUTATED   15  0   0   1   0
  DEL PEAK 20(16Q23.3) WILD-TYPE 41  1   1   0   2
D34V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 20(16Q23.3) MUTATED    9  0   0   3   0   3   0  1  0
  DEL PEAK 20(16Q23.3) WILD-TYPE 24  1   2   4   1   2   3  6  2
D34V6, multiclass
D34V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 20(16Q23.3) MUTATED             1       2        1        2        1
  DEL PEAK 20(16Q23.3) WILD-TYPE           1       8        1        3        7
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 20(16Q23.3) MUTATED           0         2         1          0
  DEL PEAK 20(16Q23.3) WILD-TYPE         3         0         4          2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 20(16Q23.3) MUTATED            4          1        0
  DEL PEAK 20(16Q23.3) WILD-TYPE          3          8        3
D34V8, multiclass

Clustering(35) Variable = Del Peak 21(17q12) mutation analysis
D35V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 21(17Q12) MUTATED   10  9
  DEL PEAK 21(17Q12) WILD-TYPE 22 25
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                          19                           47 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                           9                           25 
$`DEL PEAK 21(17Q12) MUTATED`
TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       11.87        36.03       176.55       107.34        61.18        53.92 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 
       47.84        39.62        32.19        19.56        21.67       129.24 
TCGA-EE-A2MG TCGA-EE-A2MP TCGA-EE-A3AG TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
      103.17       248.61        23.47        53.52        15.45        32.71 
TCGA-GN-A262 
      120.46 

$`DEL PEAK 21(17Q12) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JK 
      112.54        71.80       121.22        31.59        23.77        12.10 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HY 
       58.03        60.23         9.30       148.31         6.38       117.17 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       20.38        35.93       215.44        15.68        26.86       109.64 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       78.87       168.26        63.32        44.35        56.42       345.96 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2M7 
       58.75        47.54       135.91       182.01        55.59        28.80 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A3AB TCGA-EE-A3AD 
       19.76       103.27        16.96       144.76       122.73         3.68 
TCGA-EE-A3AF TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       13.81       138.77         6.41        48.59       228.59         7.76 
TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
      357.37       101.26        11.41       148.77        84.72 

  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                       11.87                         3.68 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                      248.61                       357.37 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                       47.84                        58.75 
[1] "11.9 - 248.6 (47.8)" "3.7 - 357.4 (58.8)" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A1Q5                   TCGA-D3-A1Q6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A1Q7                   TCGA-D3-A1Q9 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A2J9                   TCGA-D3-A2JD 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-D3-A2JK                   TCGA-D3-A3C6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D3-A3CE                   TCGA-D3-A3MO 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-D9-A148                   TCGA-D9-A1JX 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1HW                   TCGA-DA-A1HY 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-DA-A1I0                   TCGA-DA-A1I2 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I4                   TCGA-DA-A1I5 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A1I7                   TCGA-DA-A1I8 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-DA-A3F5                   TCGA-DA-A3F8 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A183                   TCGA-EE-A20B 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A20F                   TCGA-EE-A20H 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29A                   TCGA-EE-A29C 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29E                   TCGA-EE-A29H 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A29M                   TCGA-EE-A29P 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A29T                   TCGA-EE-A2A6 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GB                   TCGA-EE-A2GE 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GH                   TCGA-EE-A2GS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2GT                   TCGA-EE-A2M5 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A2M6                   TCGA-EE-A2M7 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2M8                   TCGA-EE-A2ME 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MG                   TCGA-EE-A2MH 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A2MK                   TCGA-EE-A2MP 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AB                   TCGA-EE-A3AD 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-EE-A3AF                   TCGA-EE-A3AG 
"DEL PEAK 21(17Q12) WILD-TYPE"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-EE-A3AH                   TCGA-ER-A19J 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1YX                   TCGA-FS-A1YY 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1Z7                   TCGA-FS-A1ZC 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZD                   TCGA-FS-A1ZF 
  "DEL PEAK 21(17Q12) MUTATED"   "DEL PEAK 21(17Q12) MUTATED" 
                  TCGA-FS-A1ZH                   TCGA-FS-A1ZM 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-FS-A1ZR                   TCGA-FS-A1ZS 
"DEL PEAK 21(17Q12) WILD-TYPE" "DEL PEAK 21(17Q12) WILD-TYPE" 
                  TCGA-GN-A262                   TCGA-GN-A265 
  "DEL PEAK 21(17Q12) MUTATED" "DEL PEAK 21(17Q12) WILD-TYPE" 
[1] "hr=" "1"  
D35V2, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 21(17Q12) MUTATED                    2             0
  DEL PEAK 21(17Q12) WILD-TYPE                  4             1
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 21(17Q12) MUTATED                                                                                          4
  DEL PEAK 21(17Q12) WILD-TYPE                                                                                        8
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 21(17Q12) MUTATED                    13
  DEL PEAK 21(17Q12) WILD-TYPE                  35
D35V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 21(17Q12) MUTATED
  DISTANT METASTASIS                                                                                                2
  PRIMARY TUMOR                                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          4
  REGIONAL LYMPH NODE                                                                                              13
                                                                                          clus
vv                                                                                         DEL PEAK 21(17Q12) WILD-TYPE
  DISTANT METASTASIS                                                                                                  4
  PRIMARY TUMOR                                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            8
  REGIONAL LYMPH NODE                                                                                                35
D35V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(17Q12) MUTATED      8   11
  DEL PEAK 21(17Q12) WILD-TYPE   14   34
        clus
vv       DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE
  FEMALE                          8                           14
  MALE                           11                           34
                              vv
clus                           M0 M1 M1A M1B M1C
  DEL PEAK 21(17Q12) MUTATED   15  0   0   0   2
  DEL PEAK 21(17Q12) WILD-TYPE 41  1   1   1   0
D35V5, multiclass
                              vv
clus                           N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 21(17Q12) MUTATED   10  0   0   3   0   2   1  1  0
  DEL PEAK 21(17Q12) WILD-TYPE 23  1   2   4   1   3   2  6  2
D35V6, multiclass
D35V7, continuous
                              vv
clus                           I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 21(17Q12) MUTATED             0       4        1        1        0
  DEL PEAK 21(17Q12) WILD-TYPE           2       6        1        4        8
                              vv
clus                           STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 21(17Q12) MUTATED           2         1         0          0
  DEL PEAK 21(17Q12) WILD-TYPE         1         1         5          2
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 21(17Q12) MUTATED            3          3        2
  DEL PEAK 21(17Q12) WILD-TYPE          4          6        1
D35V8, multiclass

Clustering(36) Variable = Del Peak 22(19p13.3) mutation analysis
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(19P13.3) MUTATED   14 10
  DEL PEAK 22(19P13.3) WILD-TYPE 18 24
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            24                             42 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            10                             24 
$`DEL PEAK 22(19P13.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D9-A148 TCGA-D9-A1JX TCGA-DA-A1HW TCGA-DA-A1I0 
       31.59        11.87       148.31         6.38        36.03        20.38 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29C 
      107.34        61.18        53.92       215.44       168.26        47.84 
TCGA-EE-A29H TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GS TCGA-EE-A2MG TCGA-EE-A2MP 
       32.19        58.75        47.54        55.59       103.17       248.61 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-GN-A262 
      122.73         3.68        53.52        15.45        32.71       120.46 

$`DEL PEAK 22(19P13.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 
      112.54        71.80       121.22        23.77        12.10        58.03 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
       60.23         9.30       117.17       176.55        35.93        15.68 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29M 
       26.86       109.64        78.87        63.32        39.62        44.35 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GT TCGA-EE-A2M5 
       56.42       345.96       135.91       182.01        19.56        21.67 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MH TCGA-EE-A2MK 
      129.24        28.80        19.76       103.27        16.96       144.76 
TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J TCGA-FS-A1YX TCGA-FS-A1YY 
       13.81        23.47       138.77         6.41        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A265 
        7.76       357.37       101.26        11.41       148.77        84.72 

  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                          3.68                           6.41 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                        248.61                         357.37 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                         53.72                          59.13 
[1] "3.7 - 248.6 (53.7)" "6.4 - 357.4 (59.1)"
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q5                     TCGA-D3-A1Q6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A1Q7                     TCGA-D3-A1Q9 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2J9                     TCGA-D3-A2JD 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-D3-A2JK                     TCGA-D3-A3C6 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D3-A3CE                     TCGA-D3-A3MO 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-D9-A148                     TCGA-D9-A1JX 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1HW                     TCGA-DA-A1HY 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I0                     TCGA-DA-A1I2 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-DA-A1I4                     TCGA-DA-A1I5 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A1I7                     TCGA-DA-A1I8 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-DA-A3F5                     TCGA-DA-A3F8 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A183                     TCGA-EE-A20B 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A20F                     TCGA-EE-A20H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29A                     TCGA-EE-A29C 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29E                     TCGA-EE-A29H 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A29M                     TCGA-EE-A29P 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A29T                     TCGA-EE-A2A6 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GB                     TCGA-EE-A2GE 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2GH                     TCGA-EE-A2GS 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A2GT                     TCGA-EE-A2M5 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M6                     TCGA-EE-A2M7 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2M8                     TCGA-EE-A2ME 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MG                     TCGA-EE-A2MH 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A2MK                     TCGA-EE-A2MP 
"DEL PEAK 22(19P13.3) WILD-TYPE"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AB                     TCGA-EE-A3AD 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-EE-A3AF                     TCGA-EE-A3AG 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-EE-A3AH                     TCGA-ER-A19J 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1YX                     TCGA-FS-A1YY 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1Z7                     TCGA-FS-A1ZC 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZD                     TCGA-FS-A1ZF 
  "DEL PEAK 22(19P13.3) MUTATED"   "DEL PEAK 22(19P13.3) MUTATED" 
                    TCGA-FS-A1ZH                     TCGA-FS-A1ZM 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-FS-A1ZR                     TCGA-FS-A1ZS 
"DEL PEAK 22(19P13.3) WILD-TYPE" "DEL PEAK 22(19P13.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 22(19P13.3) MUTATED" "DEL PEAK 22(19P13.3) WILD-TYPE" 
[1] "hr=" "1.2"
D36V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 22(19P13.3) MUTATED                    3             0
  DEL PEAK 22(19P13.3) WILD-TYPE                  3             1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 22(19P13.3) MUTATED                                                                                          4
  DEL PEAK 22(19P13.3) WILD-TYPE                                                                                        8
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 22(19P13.3) MUTATED                    17
  DEL PEAK 22(19P13.3) WILD-TYPE                  31
D36V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 22(19P13.3) MUTATED
  DISTANT METASTASIS                                                                                                  3
  PRIMARY TUMOR                                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            4
  REGIONAL LYMPH NODE                                                                                                17
                                                                                          clus
vv                                                                                         DEL PEAK 22(19P13.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    3
  PRIMARY TUMOR                                                                                                         1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              8
  REGIONAL LYMPH NODE                                                                                                  31
D36V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(19P13.3) MUTATED     10   14
  DEL PEAK 22(19P13.3) WILD-TYPE   12   31
        clus
vv       DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE
  FEMALE                           10                             12
  MALE                             14                             31
                                vv
clus                             M0 M1 M1A M1B M1C
  DEL PEAK 22(19P13.3) MUTATED   17  0   1   1   2
  DEL PEAK 22(19P13.3) WILD-TYPE 39  1   0   0   0
D36V5, multiclass
                                vv
clus                             N0 N1 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 22(19P13.3) MUTATED   10  0   1   2   1   1   1  4  1
  DEL PEAK 22(19P13.3) WILD-TYPE 23  1   1   5   0   4   2  3  1
D36V6, multiclass
D36V7, continuous
                                vv
clus                             I OR II NOS STAGE I STAGE IA STAGE IB STAGE II
  DEL PEAK 22(19P13.3) MUTATED             0       3        2        2        0
  DEL PEAK 22(19P13.3) WILD-TYPE           2       7        0        3        8
                                vv
clus                             STAGE IIA STAGE IIC STAGE III STAGE IIIA
  DEL PEAK 22(19P13.3) MUTATED           1         1         0          1
  DEL PEAK 22(19P13.3) WILD-TYPE         2         1         5          1
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 22(19P13.3) MUTATED            3          4        2
  DEL PEAK 22(19P13.3) WILD-TYPE          4          5        1
D36V8, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"      "DISTANT.METASTASIS"   "LYMPH.NODE.METASTASIS" 
                       V7                        V8 
        "TUMOR.STAGECODE"   "NEOPLASM.DISEASESTAGE" 
> q(save="no")
