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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.48.4103/CNV2ClinicalAnalysis_nozzle_onlysig_focal.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvs_onlysig.48.4103/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/404252/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215664/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         3004           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           NA           NA 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA         1555           NA           NA           NA         1354 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        1116           NA          534          451           NA         1097 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
         156           NA           NA         1155         1175          134 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
         825          366          197          272           NA           NA 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
          NA           NA           NA           NA           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           NA           NA           NA          756 
TCGA-GN-A265 
        2577 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=17,	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   11  7
  AMP PEAK  1(1Q43) WILD-TYPE  6 12
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                         18                          18 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                          7                          12 
$`AMP PEAK  1(1Q43) MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY 
       98.76        21.14        11.41        13.32         9.30        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B 
       10.03         9.99        44.52        36.69        17.56        36.07 
TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        8.81        38.63        27.12        12.03         6.48         8.94 

$`AMP PEAK  1(1Q43) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1HW 
       32.55        70.16        22.55         6.35        15.25        35.80 
TCGA-DA-A1I2 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A 
       13.68        25.15        14.83        12.20         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29H TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       37.97         4.41         4.18         8.81        24.85        84.72 

  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                       6.48                        4.18 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                      98.76                       84.72 
  AMP PEAK  1(1Q43) MUTATED AMP PEAK  1(1Q43) WILD-TYPE 
                      15.44                       15.04 
[1] "6.5 - 98.8 (15.4)" "4.2 - 84.7 (15.0)"
                 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-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-ER-A19J                  TCGA-FS-A1ZR 
"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-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-ER-A19J                  TCGA-FS-A1ZR 
"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-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-ER-A19J                  TCGA-FS-A1ZR 
"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=" "1.8"
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    6  6
  AMP PEAK  2(2Q36.2) WILD-TYPE 11 13
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                           12                            24 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                            6                            13 
$`AMP PEAK  2(2Q36.2) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-DA-A3F5 
       70.16        22.55        11.41        51.12        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
       14.83         8.81         7.96        27.12         6.48         8.94 

$`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 
       32.55        98.76        21.14         6.35        15.25        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30        35.80        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       36.69        12.20        36.07         5.13        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29P TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.41        12.03         4.18         8.81        24.85        84.72 

  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                         6.48                          4.18 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                        70.16                         98.76 
  AMP PEAK  2(2Q36.2) MUTATED AMP PEAK  2(2Q36.2) WILD-TYPE 
                       16.195                        14.465 
[1] "6.5 - 70.2 (16.2)" "4.2 - 98.8 (14.5)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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"  
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    9  4
  AMP PEAK  3(3P13) WILD-TYPE  8 15
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                         13                          23 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                          4                          15 
$`AMP PEAK  3(3P13) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F5 
       22.55        13.32        35.80         9.99        44.52        17.56 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
       14.83        36.07         5.13         4.41        27.12         6.48 
TCGA-GN-A265 
       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 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       15.25         9.30        51.12        10.03        13.68        36.69 
TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       25.15        12.20         8.81         7.96        37.97        38.63 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         8.94         4.18         8.81        24.85 

  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                       4.41                        4.18 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                      84.72                       98.76 
  AMP PEAK  3(3P13) MUTATED AMP PEAK  3(3P13) WILD-TYPE 
                      17.56                       13.68 
[1] "4.4 - 84.7 (17.6)" "4.2 - 98.8 (13.7)"
                 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-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-ER-A19J                  TCGA-FS-A1ZR 
"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-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-ER-A19J                  TCGA-FS-A1ZR 
"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-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-ER-A19J                  TCGA-FS-A1ZR 
"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=" "2.2"
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    7  6
  AMP PEAK  4(5P15.33) WILD-TYPE 10 13
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            13                             23 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             6                             13 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1I2 TCGA-DA-A1I5 
       32.55        22.55         6.35        15.25        13.68        44.52 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29T 
       17.56        36.07         8.81        38.63        27.12         6.48 
TCGA-GN-A265 
       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 
       70.16        98.76        21.14        11.41        13.32         9.30 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       35.80        51.12        10.03         9.99        36.69        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
       14.83        12.20         5.13         7.96        37.97         4.41 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         8.94         4.18         8.81        24.85 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                          6.35                           4.18 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         22.55                          12.20 
[1] "6.3 - 84.7 (22.6)" "4.2 - 98.8 (12.2)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "1.5"
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    2 12
  AMP PEAK  5(6P25.3) WILD-TYPE 15  7
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           14                            22 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                           12                             7 
$`AMP PEAK  5(6P25.3) MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1I0 
       98.76        22.55        21.14        15.25        13.32        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29P 
       13.68         9.99        12.20         8.81         7.96        12.03 
TCGA-ER-A19J TCGA-FS-A1ZR 
        4.18         8.81 

$`AMP PEAK  5(6P25.3) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3MO TCGA-DA-A1HW 
       32.55        70.16        11.41         6.35         9.30        35.80 
TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       51.12        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       36.07         5.13        37.97        38.63         4.41        27.12 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94        24.85        84.72 

  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                         4.18                          4.41 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                        98.76                         84.72 
  AMP PEAK  5(6P25.3) MUTATED AMP PEAK  5(6P25.3) WILD-TYPE 
                       12.115                        26.135 
[1] "4.2 - 98.8 (12.1)" "4.4 - 84.7 (26.1)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
  "AMP PEAK  5(6P25.3) MUTATED"   "AMP PEAK  5(6P25.3) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
"AMP PEAK  5(6P25.3) WILD-TYPE" "AMP PEAK  5(6P25.3) WILD-TYPE" 
[1] "hr=" "5"  
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   13 16
  AMP PEAK  6(7Q21.11) WILD-TYPE  4  3
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            29                              7 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                            16                              3 
$`AMP PEAK  6(7Q21.11) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
       32.55        70.16        22.55        21.14        11.41        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30        35.80        51.12        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       36.69        25.15        17.56        14.83        12.20        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
        8.81         7.96        37.97        38.63        27.12        12.03 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        6.48         8.94         4.18         8.81        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 
       98.76         6.35        15.25        10.03         5.13         4.41 
TCGA-GN-A262 
       24.85 

  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                          4.18                           4.41 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK  6(7Q21.11) MUTATED AMP PEAK  6(7Q21.11) WILD-TYPE 
                         17.56                          10.03 
[1] "4.2 - 84.7 (17.6)" "4.4 - 98.8 (10.0)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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   14 17
  AMP PEAK  7(7Q34) WILD-TYPE  3  2
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         31                           5 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                         17                           2 
$`AMP PEAK  7(7Q34) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE 
       32.55        70.16        22.55        21.14        11.41        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       44.52        36.69        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       36.07         8.81         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A265 
       84.72 

$`AMP PEAK  7(7Q34) WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-EE-A20F TCGA-GN-A262 
       98.76         6.35        15.25         5.13        24.85 

  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                       4.18                        5.13 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                      84.72                       98.76 
  AMP PEAK  7(7Q34) MUTATED AMP PEAK  7(7Q34) WILD-TYPE 
                      14.83                       15.25 
[1] "4.2 - 84.7 (14.8)" "5.1 - 98.8 (15.2)"
                 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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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    7 12
  AMP PEAK  8(8Q21.13) WILD-TYPE 10  7
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            19                             17 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                            12                              7 
$`AMP PEAK  8(8Q21.13) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO 
       70.16        22.55        11.41        15.25        13.32         9.30 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A20B 
       35.80        10.03        13.68         9.99        17.56        36.07 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR 
       37.97        38.63         4.41         6.48         4.18         8.81 
TCGA-GN-A265 
       84.72 

$`AMP PEAK  8(8Q21.13) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-DA-A1HY TCGA-DA-A1I5 
       32.55        98.76        21.14         6.35        51.12        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       36.69        25.15        14.83        12.20         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-GN-A262 
        7.96        27.12        12.03         8.94        24.85 

  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                          4.18                           5.13 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK  8(8Q21.13) MUTATED AMP PEAK  8(8Q21.13) WILD-TYPE 
                         13.68                          21.14 
[1] "4.2 - 84.7 (13.7)" "5.1 - 98.8 (21.1)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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=" "1.6"
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    7 11
  AMP PEAK  9(8Q24.21) WILD-TYPE 10  8
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            18                             18 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            11                              8 
$`AMP PEAK  9(8Q24.21) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW 
       70.16        22.55        15.25        13.32         9.30        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A20B 
       51.12        10.03        13.68         9.99        17.56        36.07 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR 
       37.97        38.63         4.41         6.48         4.18         8.81 

$`AMP PEAK  9(8Q24.21) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-DA-A1I5 
       32.55        98.76        21.14        11.41         6.35        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       36.69        25.15        14.83        12.20         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-GN-A262 TCGA-GN-A265 
        7.96        27.12        12.03         8.94        24.85        84.72 

  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                          4.18                           5.13 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                         70.16                          98.76 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        14.465                         17.985 
[1] "4.2 - 70.2 (14.5)" "5.1 - 98.8 (18.0)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "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=" "1.4"
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    2  4
  AMP PEAK 10(12Q15) WILD-TYPE 15 15
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                           6                           30 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                           4                           15 
$`AMP PEAK 10(12Q15) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A3F5 TCGA-EE-A2A6 
       70.16        22.55        15.25        35.80        17.56         8.94 

$`AMP PEAK 10(12Q15) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
       32.55        98.76        21.14        11.41         6.35        13.32 
TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       36.69        25.15        14.83        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        8.81         7.96        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       12.03         6.48         4.18         8.81        24.85        84.72 

  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                        8.94                         4.18 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                       70.16                        98.76 
  AMP PEAK 10(12Q15) MUTATED AMP PEAK 10(12Q15) WILD-TYPE 
                      20.055                       13.500 
[1] "8.9 - 70.2 (20.1)" "4.2 - 98.8 (13.5)"
                  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-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-ER-A19J                   TCGA-FS-A1ZR 
"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-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-ER-A19J                   TCGA-FS-A1ZR 
"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-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-ER-A19J                   TCGA-FS-A1ZR 
"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"  
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    5  8
  AMP PEAK 11(15Q26.2) WILD-TYPE 12 11
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                            13                             23 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                             8                             11 
$`AMP PEAK 11(15Q26.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1HW 
       32.55        22.55        21.14        11.41        13.32        35.80 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29T 
       36.69        17.56        12.20         5.13         8.81         6.48 
TCGA-GN-A265 
       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-DA-A1HY 
       70.16        98.76         6.35        15.25         9.30        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 
       10.03        13.68         9.99        44.52        25.15        14.83 
TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       36.07         7.96        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         8.94         4.18         8.81        24.85 

  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                          5.13                           4.18 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 11(15Q26.2) MUTATED AMP PEAK 11(15Q26.2) WILD-TYPE 
                         17.56                          14.83 
[1] "5.1 - 84.7 (17.6)" "4.2 - 98.8 (14.8)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "1.3"
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    9  5
  AMP PEAK 12(17Q24.3) WILD-TYPE  8 14
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                            14                             22 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                             5                             14 
$`AMP PEAK 12(17Q24.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I7 
       22.55        11.41        13.32         9.30        51.12        36.69 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P 
       17.56         5.13         8.81        37.97         4.41        12.03 
TCGA-EE-A2A6 TCGA-GN-A265 
        8.94        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 
       32.55        70.16        98.76        21.14         6.35        15.25 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       35.80        10.03        13.68         9.99        44.52        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29M 
       14.83        12.20        36.07         7.96        38.63        27.12 
TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
        6.48         4.18         8.81        24.85 

  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                          4.41                           4.18 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                         84.72                          98.76 
  AMP PEAK 12(17Q24.3) MUTATED AMP PEAK 12(17Q24.3) WILD-TYPE 
                        12.675                         18.195 
[1] "4.4 - 84.7 (12.7)" "4.2 - 98.8 (18.2)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"AMP PEAK 12(17Q24.3) WILD-TYPE" "AMP PEAK 12(17Q24.3) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 12(17Q24.3) WILD-TYPE"   "AMP PEAK 12(17Q24.3) MUTATED" 
[1] "hr=" "1.5"
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    3  4
  AMP PEAK 13(19P13.2) WILD-TYPE 14 15
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                             7                             29 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                             4                             15 
$`AMP PEAK 13(19P13.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-DA-A1I0 TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29P 
       32.55        70.16        10.03        17.56        38.63        12.03 
TCGA-ER-A19J 
        4.18 

$`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 
       98.76        22.55        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
       13.32         9.30        35.80        51.12        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       44.52        36.69        25.15        14.83        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        37.97         4.41        27.12 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94         8.81        24.85        84.72 

  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                          4.18                           4.41 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                         70.16                          98.76 
  AMP PEAK 13(19P13.2) MUTATED AMP PEAK 13(19P13.2) WILD-TYPE 
                         17.56                          14.83 
[1] "4.2 - 70.2 (17.6)" "4.4 - 98.8 (14.8)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "AMP PEAK 13(19P13.2) MUTATED" "AMP PEAK 13(19P13.2) WILD-TYPE" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"AMP PEAK 13(19P13.2) WILD-TYPE" "AMP PEAK 13(19P13.2) WILD-TYPE" 
[1] "hr=" "1"  
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    5  8
  AMP PEAK 14(22Q13.32) WILD-TYPE 12 11
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                             13                              23 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                              8                              11 
$`AMP PEAK 14(22Q13.32) MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 
       70.16        22.55        13.32         9.30        35.80        10.03 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A2A6 
       36.69        25.15        17.56         8.81        27.12         8.94 
TCGA-GN-A265 
       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 
       32.55        98.76        21.14        11.41         6.35        15.25 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A183 
       51.12        13.68         9.99        44.52        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13         7.96        37.97        38.63         4.41 
TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         4.18         8.81        24.85 

  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                           8.81                            4.18 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                          84.72                           98.76 
  AMP PEAK 14(22Q13.32) MUTATED AMP PEAK 14(22Q13.32) WILD-TYPE 
                          22.55                           13.68 
[1] "8.8 - 84.7 (22.6)" "4.2 - 98.8 (13.7)"
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"AMP PEAK 14(22Q13.32) WILD-TYPE" "AMP PEAK 14(22Q13.32) WILD-TYPE" 
                     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    4  6
  DEL PEAK  1(1P36.31) WILD-TYPE 13 13
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            10                             26 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             6                             13 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
        6.35        15.25        13.32        10.03        13.68        36.69 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83         5.13         8.81 

$`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 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
        9.30        35.80        51.12         9.99        44.52        25.15 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       12.20        36.07         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          5.13                           4.18 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         36.69                          98.76 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          13.5                           23.7 
[1] "5.1 - 36.7 (13.5)" "4.2 - 98.8 (23.7)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "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    7  8
  DEL PEAK  2(1P22.1) WILD-TYPE 10 11
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                           15                            21 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                            8                            11 
$`DEL PEAK  2(1P22.1) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1I0 TCGA-DA-A1I2 
       22.55        11.41        13.32         9.30        10.03        13.68 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20H 
       36.69        25.15        17.56        14.83        36.07         8.81 
TCGA-EE-A29C TCGA-EE-A29T TCGA-GN-A262 
       37.97         6.48        24.85 

$`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 
       32.55        70.16        98.76        21.14         6.35        15.25 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-EE-A183 TCGA-EE-A20F 
       35.80        51.12         9.99        44.52        12.20         5.13 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 
        7.96        38.63         4.41        27.12        12.03         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        84.72 

  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                         6.48                          4.18 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        37.97                         98.76 
  DEL PEAK  2(1P22.1) MUTATED DEL PEAK  2(1P22.1) WILD-TYPE 
                        14.83                         15.25 
[1] "6.5 - 38.0 (14.8)" "4.2 - 98.8 (15.2)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  2(1P22.1) WILD-TYPE" "DEL PEAK  2(1P22.1) WILD-TYPE" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  2(1P22.1) MUTATED" "DEL PEAK  2(1P22.1) WILD-TYPE" 
[1] "hr=" "1.1"
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    5  5
  DEL PEAK  3(2Q37.3) WILD-TYPE 12 14
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                           10                            26 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            5                            14 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1I0 TCGA-EE-A20B TCGA-EE-A20F 
       11.41         6.35        15.25        10.03        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P 
        8.81        37.97        38.63        12.03 

$`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 
       32.55        70.16        98.76        22.55        21.14        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30        35.80        51.12        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A 
       36.69        25.15        17.56        14.83        12.20         7.96 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        4.41        27.12         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         5.13                          4.18 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        38.63                         98.76 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        11.72                         19.35 
[1] "5.1 - 38.6 (11.7)" "4.2 - 98.8 (19.4)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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=" "1.2"
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    6  5
  DEL PEAK  4(3P26.1) WILD-TYPE 11 14
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                           11                            25 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                            5                            14 
$`DEL PEAK  4(3P26.1) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        98.76        22.55        15.25        35.80        13.68 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-GN-A262 
       44.52        36.69         5.13        12.03        24.85 

$`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 
       70.16        21.14        11.41         6.35        13.32         9.30 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       51.12        10.03         9.99        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       12.20        36.07         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        4.41        27.12         6.48         8.94         4.18         8.81 
TCGA-GN-A265 
       84.72 

  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                         5.13                          4.18 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                        98.76                         84.72 
  DEL PEAK  4(3P26.1) MUTATED DEL PEAK  4(3P26.1) WILD-TYPE 
                        24.85                         12.20 
[1] "5.1 - 98.8 (24.9)" "4.2 - 84.7 (12.2)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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=" "1.8"
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    6  3
  DEL PEAK  5(3Q27.2) WILD-TYPE 11 16
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                            9                            27 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                            3                            16 
$`DEL PEAK  5(3Q27.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 
       32.55        98.76        35.80        13.68        44.52        36.69 
TCGA-EE-A29H TCGA-EE-A29P TCGA-GN-A262 
        4.41        12.03        24.85 

$`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 
       70.16        22.55        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 
       13.32         9.30        51.12        10.03         9.99        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
        7.96        37.97        38.63        27.12         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        84.72 

  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                         4.41                          4.18 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                        98.76                         84.72 
  DEL PEAK  5(3Q27.2) MUTATED DEL PEAK  5(3Q27.2) WILD-TYPE 
                        32.55                         13.32 
[1] "4.4 - 98.8 (32.5)" "4.2 - 84.7 (13.3)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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=" "2.6"
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    7  3
  DEL PEAK  6(4P16.3) WILD-TYPE 10 16
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                           10                            26 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                            3                            16 
$`DEL PEAK  6(4P16.3) MUTATED`
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
        9.30        35.80        14.83        36.07         5.13        37.97 
TCGA-EE-A29H TCGA-EE-A29M TCGA-FS-A1ZR TCGA-GN-A262 
        4.41        27.12         8.81        24.85 

$`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 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        6.35        15.25        13.32        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 
        9.99        44.52        36.69        25.15        17.56        12.20 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        8.81         7.96        38.63        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-GN-A265 
        4.18        84.72 

  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                         4.41                          4.18 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                        37.97                         98.76 
  DEL PEAK  6(4P16.3) MUTATED DEL PEAK  6(4P16.3) WILD-TYPE 
                       19.840                        14.465 
[1] "4.4 - 38.0 (19.8)" "4.2 - 98.8 (14.5)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK  6(4P16.3) WILD-TYPE"   "DEL PEAK  6(4P16.3) MUTATED" 
                   TCGA-GN-A262                    TCGA-GN-A265 
  "DEL PEAK  6(4P16.3) MUTATED" "DEL PEAK  6(4P16.3) WILD-TYPE" 
[1] "hr=" "1.9"
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    9  3
  DEL PEAK  7(4Q34.3) WILD-TYPE  8 16
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                           12                            24 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                            3                            16 
$`DEL PEAK  7(4Q34.3) MUTATED`
TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
       11.41        35.80        51.12        36.69        17.56        14.83 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
       36.07         8.81        37.97        27.12         6.48         8.94 

$`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 
       32.55        70.16        98.76        22.55        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       15.25        13.32         9.30        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29E 
       44.52        25.15        12.20         5.13         7.96        38.63 
TCGA-EE-A29H TCGA-EE-A29P TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.41        12.03         4.18         8.81        24.85        84.72 

  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                         6.48                          4.18 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        51.12                         98.76 
  DEL PEAK  7(4Q34.3) MUTATED DEL PEAK  7(4Q34.3) WILD-TYPE 
                        22.34                         13.50 
[1] "6.5 - 51.1 (22.3)" "4.2 - 98.8 (13.5)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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=" "3.1"
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    8  7
  DEL PEAK  8(5Q11.2) WILD-TYPE  9 12
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                           15                            21 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                            7                            12 
$`DEL PEAK  8(5Q11.2) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I0 
       22.55        11.41         6.35        15.25        35.80        10.03 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E 
       44.52        36.69        17.56         8.81        37.97        38.63 
TCGA-EE-A29M TCGA-EE-A29P TCGA-GN-A262 
       27.12        12.03        24.85 

$`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 
       32.55        70.16        98.76        21.14        13.32         9.30 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
       51.12        13.68         9.99        25.15        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2A6 
       36.07         5.13         7.96         4.41         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        84.72 

  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                         6.35                          4.18 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                        44.52                         98.76 
  DEL PEAK  8(5Q11.2) MUTATED DEL PEAK  8(5Q11.2) WILD-TYPE 
                        22.55                         13.32 
[1] "6.3 - 44.5 (22.6)" "4.2 - 98.8 (13.3)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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    9  8
  DEL PEAK  9(5Q31.3) WILD-TYPE  8 11
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                           17                            19 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                            8                            11 
$`DEL PEAK  9(5Q31.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1HY 
       22.55        11.41         6.35        15.25        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20H 
       10.03        44.52        36.69        25.15        17.56         8.81 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-GN-A262 
       37.97        38.63        27.12        12.03        24.85 

$`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 
       32.55        70.16        98.76        21.14        13.32         9.30 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       13.68         9.99        14.83        12.20        36.07         5.13 
TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        7.96         4.41         6.48         8.94         4.18         8.81 
TCGA-GN-A265 
       84.72 

  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                         6.35                          4.18 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                        51.12                         98.76 
  DEL PEAK  9(5Q31.3) MUTATED DEL PEAK  9(5Q31.3) WILD-TYPE 
                        24.85                         12.20 
[1] "6.3 - 51.1 (24.9)" "4.2 - 98.8 (12.2)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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-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-ER-A19J                    TCGA-FS-A1ZR 
"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=" "1.7"
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   10 12
  DEL PEAK 10(6Q25.2) WILD-TYPE  7  7
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           22                            14 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                           12                             7 
$`DEL PEAK 10(6Q25.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HY 
       32.55        22.55        11.41        15.25        13.32        51.12 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B 
        9.99        36.69        25.15        17.56        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        37.97         4.41        27.12 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        6.48         8.94         4.18         8.81 

$`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 
       70.16        98.76        21.14         6.35         9.30        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A29E TCGA-EE-A29P 
       10.03        13.68        44.52        14.83        38.63        12.03 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                         4.18                          6.35 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                        51.12                         98.76 
  DEL PEAK 10(6Q25.2) MUTATED DEL PEAK 10(6Q25.2) WILD-TYPE 
                       12.760                        22.995 
[1] "4.2 - 51.1 (12.8)" "6.3 - 98.8 (23.0)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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=" "1.8"
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    9 12
  DEL PEAK 11(6Q27) WILD-TYPE  8  7
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         21                          15 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                         12                           7 
$`DEL PEAK 11(6Q27) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HY 
       32.55        22.55        11.41        15.25        13.32        51.12 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B 
        9.99        36.69        25.15        17.56        12.20        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
        8.81         7.96        37.97         4.41        27.12         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        8.94         4.18         8.81 

$`DEL PEAK 11(6Q27) WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3MO TCGA-DA-A1HW 
       70.16        98.76        21.14         6.35         9.30        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A20F TCGA-EE-A29E 
       10.03        13.68        44.52        14.83         5.13        38.63 
TCGA-EE-A29P TCGA-GN-A262 TCGA-GN-A265 
       12.03        24.85        84.72 

  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                       4.18                        5.13 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                      51.12                       98.76 
  DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE 
                      13.32                       21.14 
[1] "4.2 - 51.1 (13.3)" "5.1 - 98.8 (21.1)"
                 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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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-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-ER-A19J                  TCGA-FS-A1ZR 
  "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=" "1.8"
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   13 14
  DEL PEAK 12(9P21.3) WILD-TYPE  4  5
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           27                             9 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           14                             5 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO 
       32.55        70.16         6.35        15.25        13.32         9.30 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       35.80        51.12        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       25.15        17.56        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       37.97        38.63         4.41        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        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 
       98.76        22.55        21.14        11.41        10.03        14.83 
TCGA-EE-A183 TCGA-EE-A29M TCGA-GN-A262 
       12.20        27.12        24.85 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         4.18                         10.03 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        84.72                         98.76 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                        13.68                         21.14 
[1] "4.2 - 84.7 (13.7)"  "10.0 - 98.8 (21.1)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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-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-ER-A19J                    TCGA-FS-A1ZR 
  "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=" "1.1"
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    7  9
  DEL PEAK 13(9Q21.2) WILD-TYPE 10 10
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                           16                            20 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                            9                            10 
$`DEL PEAK 13(9Q21.2) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       32.55        15.25         9.30        35.80        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       44.52        25.15        17.56        36.07         5.13         8.81 
TCGA-EE-A29P TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       12.03         8.81        24.85        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 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A183 
       13.32        51.12        10.03        36.69        14.83        12.20 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
        7.96        37.97        38.63         4.41        27.12         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J 
        8.94         4.18 

  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                         5.13                          4.18 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                        84.72                         98.76 
  DEL PEAK 13(9Q21.2) MUTATED DEL PEAK 13(9Q21.2) WILD-TYPE 
                       16.405                        14.075 
[1] "5.1 - 84.7 (16.4)" "4.2 - 98.8 (14.1)"
                   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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "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-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-ER-A19J                    TCGA-FS-A1ZR 
"DEL PEAK 13(9Q21.2) WILD-TYPE"   "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=" "1.1"
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   12 14
  DEL PEAK 14(10Q21.1) WILD-TYPE  5  5
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            26                             10 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                            14                              5 
$`DEL PEAK 14(10Q21.1) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        22.55        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       15.25        13.32         9.30        35.80        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B 
       44.52        36.69        25.15        17.56        14.83        36.07 
TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        8.81         4.41        27.12        12.03         6.48         8.94 
TCGA-FS-A1ZR TCGA-GN-A262 
        8.81        24.85 

$`DEL PEAK 14(10Q21.1) WILD-TYPE`
TCGA-D3-A2J9 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A 
       21.14        51.12        10.03        12.20         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-ER-A19J TCGA-GN-A265 
       37.97        38.63         4.18        84.72 

  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                          4.41                           4.18 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                         98.76                          84.72 
  DEL PEAK 14(10Q21.1) MUTATED DEL PEAK 14(10Q21.1) WILD-TYPE 
                         15.04                          16.67 
[1] "4.4 - 98.8 (15.0)" "4.2 - 84.7 (16.7)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 14(10Q21.1) WILD-TYPE"   "DEL PEAK 14(10Q21.1) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
  "DEL PEAK 14(10Q21.1) MUTATED" "DEL PEAK 14(10Q21.1) WILD-TYPE" 
[1] "hr=" "1.1"
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   13 14
  DEL PEAK 15(10Q23.31) WILD-TYPE  4  5
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             27                               9 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             14                               5 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        22.55        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       15.25        13.32         9.30        35.80        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B 
       44.52        36.69        25.15        17.56        14.83        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
        5.13         8.81         4.41        27.12        12.03         6.48 
TCGA-EE-A2A6 TCGA-FS-A1ZR TCGA-GN-A262 
        8.94         8.81        24.85 

$`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 
       21.14        51.12        10.03        12.20         7.96        37.97 
TCGA-EE-A29E TCGA-ER-A19J TCGA-GN-A265 
       38.63         4.18        84.72 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           4.41                            4.18 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                          98.76                           84.72 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                          14.83                           21.14 
[1] "4.4 - 98.8 (14.8)" "4.2 - 84.7 (21.1)"
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"DEL PEAK 15(10Q23.31) WILD-TYPE"   "DEL PEAK 15(10Q23.31) MUTATED" 
                     TCGA-GN-A262                      TCGA-GN-A265 
  "DEL PEAK 15(10Q23.31) MUTATED" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.1"
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   12 10
  DEL PEAK 16(11Q22.3) WILD-TYPE  5  9
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            22                             14 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                            10                              9 
$`DEL PEAK 16(11Q22.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3MO 
       32.55        98.76        22.55        11.41        15.25         9.30 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20B 
       35.80        10.03        44.52        25.15        17.56        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        37.97         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-GN-A262 TCGA-GN-A265 
       12.03         6.48        24.85        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 
       70.16        21.14         6.35        13.32        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29E TCGA-EE-A2A6 
        9.99        36.69        14.83        12.20        38.63         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR 
        4.18         8.81 

  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                          4.41                           4.18 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                         98.76                          70.16 
  DEL PEAK 16(11Q22.3) MUTATED DEL PEAK 16(11Q22.3) WILD-TYPE 
                        20.055                         13.500 
[1] "4.4 - 98.8 (20.1)" "4.2 - 70.2 (13.5)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "1.6"
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    1  2
  DEL PEAK 17(12Q24.32) WILD-TYPE 16 17
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                              3                              33 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                              2                              17 
$`DEL PEAK 17(12Q24.32) MUTATED`
TCGA-D3-A3C6 TCGA-EE-A20B TCGA-EE-A20H 
       15.25        36.07         8.81 

$`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 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       14.83        12.20         5.13         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                           8.81                            4.18 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                          36.07                           98.76 
  DEL PEAK 17(12Q24.32) MUTATED DEL PEAK 17(12Q24.32) WILD-TYPE 
                          15.25                           14.83 
[1] "8.8 - 36.1 (15.2)" "4.2 - 98.8 (14.8)"
                     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-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-ER-A19J                      TCGA-FS-A1ZR 
"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-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-ER-A19J                      TCGA-FS-A1ZR 
"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-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-ER-A19J                      TCGA-FS-A1ZR 
"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=" "1.3"
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    7  3
  DEL PEAK 18(14Q31.1) WILD-TYPE 10 16
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                            10                             26 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                             3                             16 
$`DEL PEAK 18(14Q31.1) MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A29C 
       13.32        51.12        44.52        25.15        17.56        37.97 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-FS-A1ZR 
       12.03         6.48         8.94         8.81 

$`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 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        6.35        15.25         9.30        35.80        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
        9.99        36.69        14.83        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-ER-A19J 
        8.81         7.96        38.63         4.41        27.12         4.18 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                          6.48                           4.18 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                         51.12                          98.76 
  DEL PEAK 18(14Q31.1) MUTATED DEL PEAK 18(14Q31.1) WILD-TYPE 
                         15.44                          15.04 
[1] "6.5 - 51.1 (15.4)" "4.2 - 98.8 (15.0)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"DEL PEAK 18(14Q31.1) WILD-TYPE"   "DEL PEAK 18(14Q31.1) MUTATED" 
                    TCGA-GN-A262                     TCGA-GN-A265 
"DEL PEAK 18(14Q31.1) WILD-TYPE" "DEL PEAK 18(14Q31.1) WILD-TYPE" 
[1] "hr=" "2"  
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    1  5
  DEL PEAK 19(15Q21.1) WILD-TYPE 16 14
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             6                             30 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             5                             14 
$`DEL PEAK 19(15Q21.1) MUTATED`
TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I8 TCGA-EE-A183 TCGA-EE-A29P TCGA-ER-A19J 
       15.25        35.80        25.15        12.20        12.03         4.18 

$`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 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        6.35        13.32         9.30        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A20B 
        9.99        44.52        36.69        17.56        14.83        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        5.13         8.81         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       27.12         6.48         8.94         8.81        24.85        84.72 

  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                          4.18                           4.41 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                         35.80                          98.76 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                        13.725                         16.195 
[1] "4.2 - 35.8 (13.7)" "4.4 - 98.8 (16.2)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
  "DEL PEAK 19(15Q21.1) MUTATED" "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "DEL PEAK 19(15Q21.1) MUTATED" "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-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-ER-A19J                     TCGA-FS-A1ZR 
  "DEL PEAK 19(15Q21.1) MUTATED" "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=" "2.1"
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    6  5
  DEL PEAK 20(16Q23.3) WILD-TYPE 11 14
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                            11                             25 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                             5                             14 
$`DEL PEAK 20(16Q23.3) MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 
       32.55        98.76        13.32        35.80        13.68         9.99 
TCGA-DA-A3F8 TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-GN-A262 
       14.83         4.41        27.12        12.03        24.85 

$`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 
       70.16        22.55        21.14        11.41         6.35        15.25 
TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
        9.30        51.12        10.03        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       17.56        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       37.97        38.63         6.48         8.94         4.18         8.81 
TCGA-GN-A265 
       84.72 

  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                          4.41                           4.18 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                         98.76                          84.72 
  DEL PEAK 20(16Q23.3) MUTATED DEL PEAK 20(16Q23.3) WILD-TYPE 
                         14.83                          15.25 
[1] "4.4 - 98.8 (14.8)" "4.2 - 84.7 (15.2)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "1.4"
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    6  4
  DEL PEAK 21(17Q12) WILD-TYPE 11 15
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                          10                           26 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                           4                           15 
$`DEL PEAK 21(17Q12) MUTATED`
TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       11.41        35.80        13.68        44.52        36.69        25.15 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-GN-A262 
       37.97        38.63         4.41        24.85 

$`DEL PEAK 21(17Q12) WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JK 
       32.55        70.16        98.76        22.55        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 
       15.25        13.32         9.30        51.12        10.03         9.99 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        7.96        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A265 
        8.81        84.72 

  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                        4.41                         4.18 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                       44.52                        98.76 
  DEL PEAK 21(17Q12) MUTATED DEL PEAK 21(17Q12) WILD-TYPE 
                      30.475                       12.760 
[1] "4.4 - 44.5 (30.5)" "4.2 - 98.8 (12.8)"
                  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-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-ER-A19J                   TCGA-FS-A1ZR 
"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-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-ER-A19J                   TCGA-FS-A1ZR 
"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-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-ER-A19J                   TCGA-FS-A1ZR 
"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=" "2.1"
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    7  6
  DEL PEAK 22(19P13.3) WILD-TYPE 10 13
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                            13                             23 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                             6                             13 
$`DEL PEAK 22(19P13.3) MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       22.55        11.41        35.80        10.03        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A2A6 
       25.15        17.56         8.81        37.97         4.41         8.94 
TCGA-GN-A262 
       24.85 

$`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 
       32.55        70.16        98.76        21.14         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
       13.32         9.30        51.12        13.68         9.99        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29M 
       12.20        36.07         5.13         7.96        38.63        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
       12.03         6.48         4.18         8.81        84.72 

  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                          4.41                           4.18 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                         44.52                          98.76 
  DEL PEAK 22(19P13.3) MUTATED DEL PEAK 22(19P13.3) WILD-TYPE 
                         22.55                          13.68 
[1] "4.4 - 44.5 (22.6)" "4.2 - 98.8 (13.7)"
                    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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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-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-ER-A19J                     TCGA-FS-A1ZR 
"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=" "1.3"
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")
