
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/404040/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-WT/3215660/SKCM-WT.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-WT", "-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-WT"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=23, in cluster file=35, common to both=23
[1] 20 23
[1] "Amp Peak  1(1p12) mutation analysis"
[1] 3
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                          9                          14 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                          9                          14 
[1] "Amp Peak  2(1q44) mutation analysis"
[1] 3
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         11                          12 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                         11                          12 
[1] "Amp Peak  3(4q12) mutation analysis"
[1] 3
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                          8                          15 
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                          8                          15 
[1] "Amp Peak  4(5p15.33) mutation analysis"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             7                             16 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             7                             16 
[1] "Amp Peak  5(5q35.3) mutation analysis"
[1] 3
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                            18 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            5                            18 
[1] "Amp Peak  6(8q11.21) mutation analysis"
[1] 3
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                            12                             11 
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                            12                             11 
[1] "Amp Peak  7(11q13.3) mutation analysis"
[1] 3
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                             5                             18 
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                             5                             18 
[1] "Amp Peak  8(11q13.3) mutation analysis"
[1] 3
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                             5                             18 
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                             5                             18 
[1] "Amp Peak  9(12q14.1) mutation analysis"
[1] 3
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            10                             13 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                            10                             13 
[1] "Amp Peak 10(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                            10                             13 
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                            10                             13 
[1] "Amp Peak 11(22q13.1) mutation analysis"
[1] 3
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                            12                             11 
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                            12                             11 
[1] "Amp Peak 12(Xq28) mutation analysis"
[1] 3
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          8                          15 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          8                          15 
[1] "Del Peak 1(2q37.3) mutation analysis"
[1] 3
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                           7                           16 
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                           7                           16 
[1] "Del Peak 2(4q34.3) mutation analysis"
[1] 3
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           7                           16 
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           7                           16 
[1] "Del Peak 3(5p15.31) mutation analysis"
[1] 3
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            5                            18 
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            5                            18 
[1] "Del Peak 4(9p21.3) mutation analysis"
[1] 3
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                          14                            9 
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                          14                            9 
[1] "Del Peak 5(10q26.3) mutation analysis"
[1] 3
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                           13                            10 
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                           13                            10 
[1] "Del Peak 6(11q23.3) mutation analysis"
[1] 3
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                           14                             9 
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                           14                             9 
[1] "Del Peak 7(15q14) mutation analysis"
[1] 3
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                          9                          14 
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                          9                          14 
[1] "Del Peak 8(16p13.3) mutation analysis"
[1] 3
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            4                            19 
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            4                            19 
[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 23 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-DA-A3F2 
          NA         1390           NA           NA           NA          589 
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        2386          200           NA           NA           NA           NA 
TCGA-FS-A1ZU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=14,	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=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T1 T1A  T2 T2A T3A T3B  T4 T4A T4B  TX 
  2   1   2   1   3   2   1   2   5   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 23 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=6, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak  1(1p12) mutation analysis
D1V1, survival
                             sevent
clus2                         0 1
  AMP PEAK  1(1P12) MUTATED   1 4
  AMP PEAK  1(1P12) WILD-TYPE 4 5
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                          5                           9 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                          4                           5 
$`AMP PEAK  1(1P12) MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29D TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A264 
       10.26        11.15        12.99         6.58        31.33 

$`AMP PEAK  1(1P12) WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 
       45.70        24.00         4.93        19.36         6.31        78.44 
TCGA-GN-A261 TCGA-GN-A26A TCGA-GN-A26D 
       15.35        12.16        14.70 

  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                       6.58                        4.93 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      31.33                       78.44 
  AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE 
                      11.15                       15.35 
[1] "6.6 - 31.3 (11.2)" "4.9 - 78.4 (15.3)"
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
  "AMP PEAK  1(1P12) MUTATED" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  1(1P12) MUTATED"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  1(1P12) WILD-TYPE"   "AMP PEAK  1(1P12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  1(1P12) WILD-TYPE" "AMP PEAK  1(1P12) WILD-TYPE" 
[1] "hr=" "2"  
D1V2, continuous
                             vv
clus                          DISTANT METASTASIS
  AMP PEAK  1(1P12) MUTATED                    2
  AMP PEAK  1(1P12) WILD-TYPE                  1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  1(1P12) MUTATED                                                                                          1
  AMP PEAK  1(1P12) WILD-TYPE                                                                                        5
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  1(1P12) MUTATED                     6
  AMP PEAK  1(1P12) WILD-TYPE                   8
D1V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  1(1P12) MUTATED
  DISTANT METASTASIS                                                                                               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         1
  REGIONAL LYMPH NODE                                                                                              6
                                                                                          clus
vv                                                                                         AMP PEAK  1(1P12) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                                8
D1V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  1(1P12) MUTATED      2    7
  AMP PEAK  1(1P12) WILD-TYPE   10    4
        clus
vv       AMP PEAK  1(1P12) MUTATED AMP PEAK  1(1P12) WILD-TYPE
  FEMALE                         2                          10
  MALE                           7                           4
                             vv
clus                          N0 N1 N1A N1B N2B N3
  AMP PEAK  1(1P12) MUTATED    5  0   1   1   0  0
  AMP PEAK  1(1P12) WILD-TYPE  6  1   1   2   2  2
D1V5, multiclass
D1V6, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  1(1P12) MUTATED         1        1        1         1         1
  AMP PEAK  1(1P12) WILD-TYPE       3        0        0         1         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  1(1P12) MUTATED           0          1          0          1
  AMP PEAK  1(1P12) WILD-TYPE         1          1          2          3
D1V7, multiclass

Clustering(2) Variable = Amp Peak  2(1q44) mutation analysis
D2V1, survival
                             sevent
clus2                         0 1
  AMP PEAK  2(1Q44) MUTATED   2 4
  AMP PEAK  2(1Q44) WILD-TYPE 3 5
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                          6                           8 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                          4                           5 
$`AMP PEAK  2(1Q44) MUTATED`
TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A3ET TCGA-GN-A26A TCGA-GN-A26D 
        4.93         6.31        11.15         6.58        12.16        14.70 

$`AMP PEAK  2(1Q44) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-ER-A19L TCGA-ER-A1A1 
       10.26        45.70        24.00        19.36        12.99        78.44 
TCGA-GN-A261 TCGA-GN-A264 
       15.35        31.33 

  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                       4.93                       10.26 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                      14.70                       78.44 
  AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE 
                      8.865                      21.680 
[1] "4.9 - 14.7 (8.9)"   "10.3 - 78.4 (21.7)"
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK  2(1Q44) MUTATED" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  2(1Q44) WILD-TYPE"   "AMP PEAK  2(1Q44) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  2(1Q44) WILD-TYPE" "AMP PEAK  2(1Q44) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
  "AMP PEAK  2(1Q44) MUTATED"   "AMP PEAK  2(1Q44) MUTATED" 
[1] "hr=" "5.5"
D2V2, continuous
                             vv
clus                          DISTANT METASTASIS
  AMP PEAK  2(1Q44) MUTATED                    3
  AMP PEAK  2(1Q44) WILD-TYPE                  0
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  2(1Q44) MUTATED                                                                                          2
  AMP PEAK  2(1Q44) WILD-TYPE                                                                                        4
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  2(1Q44) MUTATED                     6
  AMP PEAK  2(1Q44) WILD-TYPE                   8
D2V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  2(1Q44) MUTATED
  DISTANT METASTASIS                                                                                               3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         2
  REGIONAL LYMPH NODE                                                                                              6
                                                                                          clus
vv                                                                                         AMP PEAK  2(1Q44) WILD-TYPE
  DISTANT METASTASIS                                                                                                 0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                8
D2V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1Q44) MUTATED      6    5
  AMP PEAK  2(1Q44) WILD-TYPE    6    6
        clus
vv       AMP PEAK  2(1Q44) MUTATED AMP PEAK  2(1Q44) WILD-TYPE
  FEMALE                         6                           6
  MALE                           5                           6
                             vv
clus                          N0 N1 N1A N1B N2B N3
  AMP PEAK  2(1Q44) MUTATED    7  0   2   2   0  0
  AMP PEAK  2(1Q44) WILD-TYPE  4  1   0   1   2  2
D2V5, multiclass
D2V6, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  2(1Q44) MUTATED         2        1        1         1         2
  AMP PEAK  2(1Q44) WILD-TYPE       2        0        0         1         1
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q44) MUTATED           0          2          1          1
  AMP PEAK  2(1Q44) WILD-TYPE         1          0          1          3
D2V7, multiclass

Clustering(3) Variable = Amp Peak  3(4q12) mutation analysis
D3V1, survival
                             sevent
clus2                         0 1
  AMP PEAK  3(4Q12) MUTATED   2 1
  AMP PEAK  3(4Q12) WILD-TYPE 3 8
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                          3                          11 
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                          1                           8 
$`AMP PEAK  3(4Q12) MUTATED`
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26D 
        6.58        31.33        14.70 

$`AMP PEAK  3(4Q12) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A26A 
       11.15        12.99        78.44        15.35        12.16 

  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                       6.58                        4.93 
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                      31.33                       78.44 
  AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE 
                      14.70                       12.99 
[1] "6.6 - 31.3 (14.7)" "4.9 - 78.4 (13.0)"
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"AMP PEAK  3(4Q12) WILD-TYPE" "AMP PEAK  3(4Q12) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK  3(4Q12) WILD-TYPE"   "AMP PEAK  3(4Q12) MUTATED" 
[1] "hr=" "2.4"
D3V2, continuous
                             vv
clus                          DISTANT METASTASIS
  AMP PEAK  3(4Q12) MUTATED                    2
  AMP PEAK  3(4Q12) WILD-TYPE                  1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  3(4Q12) MUTATED                                                                                          1
  AMP PEAK  3(4Q12) WILD-TYPE                                                                                        5
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK  3(4Q12) MUTATED                     5
  AMP PEAK  3(4Q12) WILD-TYPE                   9
D3V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  3(4Q12) MUTATED
  DISTANT METASTASIS                                                                                               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         1
  REGIONAL LYMPH NODE                                                                                              5
                                                                                          clus
vv                                                                                         AMP PEAK  3(4Q12) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                                9
D3V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(4Q12) MUTATED      4    4
  AMP PEAK  3(4Q12) WILD-TYPE    8    7
        clus
vv       AMP PEAK  3(4Q12) MUTATED AMP PEAK  3(4Q12) WILD-TYPE
  FEMALE                         4                           8
  MALE                           4                           7
                             vv
clus                          N0 N1 N1A N1B N2B N3
  AMP PEAK  3(4Q12) MUTATED    6  0   1   0   0  0
  AMP PEAK  3(4Q12) WILD-TYPE  5  1   1   3   2  2
D3V5, multiclass
D3V6, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  3(4Q12) MUTATED         2        1        1         0         2
  AMP PEAK  3(4Q12) WILD-TYPE       2        0        0         2         1
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  3(4Q12) MUTATED           0          1          0          0
  AMP PEAK  3(4Q12) WILD-TYPE         1          1          2          4
D3V7, multiclass

Clustering(4) Variable = Amp Peak  4(5p15.33) mutation analysis
D4V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  4(5P15.33) MUTATED   2 3
  AMP PEAK  4(5P15.33) WILD-TYPE 3 6
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             5                              9 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                             3                              6 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-EE-A29D TCGA-GN-A264 TCGA-GN-A26D 
       45.70        24.00        11.15        31.33        14.70 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-D3-A2J6 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A1A1 
       10.26         4.93        19.36         6.31        12.99        78.44 
TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A 
        6.58        15.35        12.16 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         11.15                           4.93 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         45.70                          78.44 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         24.00                          12.16 
[1] "11.2 - 45.7 (24.0)" "4.9 - 78.4 (12.2)" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  4(5P15.33) MUTATED" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  4(5P15.33) WILD-TYPE" "AMP PEAK  4(5P15.33) WILD-TYPE" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  4(5P15.33) WILD-TYPE"   "AMP PEAK  4(5P15.33) MUTATED" 
[1] "hr=" "2.1"
D4V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK  4(5P15.33) MUTATED                    1
  AMP PEAK  4(5P15.33) WILD-TYPE                  2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  4(5P15.33) MUTATED                                                                                          1
  AMP PEAK  4(5P15.33) WILD-TYPE                                                                                        5
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  4(5P15.33) MUTATED                     5
  AMP PEAK  4(5P15.33) WILD-TYPE                   9
D4V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  4(5P15.33) MUTATED
  DISTANT METASTASIS                                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 5
                                                                                          clus
vv                                                                                         AMP PEAK  4(5P15.33) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              5
  REGIONAL LYMPH NODE                                                                                                   9
D4V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      4    3
  AMP PEAK  4(5P15.33) WILD-TYPE    8    8
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                            4                              8
  MALE                              3                              8
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK  4(5P15.33) MUTATED    3  0   0   1   1  1
  AMP PEAK  4(5P15.33) WILD-TYPE  8  1   2   2   1  1
D4V5, multiclass
D4V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  4(5P15.33) MUTATED         0        0        1         0         2
  AMP PEAK  4(5P15.33) WILD-TYPE       4        1        0         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  4(5P15.33) MUTATED           0          0          0          3
  AMP PEAK  4(5P15.33) WILD-TYPE         1          2          2          1
D4V7, multiclass

Clustering(5) Variable = Amp Peak  5(5q35.3) mutation analysis
D5V1, survival
                               sevent
clus2                           0 1
  AMP PEAK  5(5Q35.3) MUTATED   1 2
  AMP PEAK  5(5Q35.3) WILD-TYPE 4 7
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            3                            11 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                            2                             7 
$`AMP PEAK  5(5Q35.3) MUTATED`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-ER-A3ET 
       24.00         4.93         6.58 

$`AMP PEAK  5(5Q35.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       10.26        45.70        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       78.44        15.35        31.33        12.16        14.70 

  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         4.93                          6.31 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                        24.00                         78.44 
  AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE 
                         6.58                         14.70 
[1] "4.9 - 24.0 (6.6)"  "6.3 - 78.4 (14.7)"
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "AMP PEAK  5(5Q35.3) MUTATED"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"AMP PEAK  5(5Q35.3) WILD-TYPE"   "AMP PEAK  5(5Q35.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"AMP PEAK  5(5Q35.3) WILD-TYPE" "AMP PEAK  5(5Q35.3) WILD-TYPE" 
[1] "hr=" "1.9"
D5V2, continuous
                               vv
clus                            DISTANT METASTASIS
  AMP PEAK  5(5Q35.3) MUTATED                    2
  AMP PEAK  5(5Q35.3) WILD-TYPE                  1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  5(5Q35.3) MUTATED                                                                                          1
  AMP PEAK  5(5Q35.3) WILD-TYPE                                                                                        5
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK  5(5Q35.3) MUTATED                     2
  AMP PEAK  5(5Q35.3) WILD-TYPE                  12
D5V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  5(5Q35.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                                2
                                                                                          clus
vv                                                                                         AMP PEAK  5(5Q35.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             5
  REGIONAL LYMPH NODE                                                                                                 12
D5V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.3) MUTATED      4    1
  AMP PEAK  5(5Q35.3) WILD-TYPE    8   10
        clus
vv       AMP PEAK  5(5Q35.3) MUTATED AMP PEAK  5(5Q35.3) WILD-TYPE
  FEMALE                           4                             8
  MALE                             1                            10
                               vv
clus                            N0 N1 N1A N1B N2B N3
  AMP PEAK  5(5Q35.3) MUTATED    2  0   1   1   0  1
  AMP PEAK  5(5Q35.3) WILD-TYPE  9  1   1   2   2  1
D5V5, multiclass
D5V6, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  5(5Q35.3) MUTATED         1        0        1         0         0
  AMP PEAK  5(5Q35.3) WILD-TYPE       3        1        0         2         3
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  5(5Q35.3) MUTATED           0          1          1          1
  AMP PEAK  5(5Q35.3) WILD-TYPE         1          1          1          3
D5V7, multiclass

Clustering(6) Variable = Amp Peak  6(8q11.21) mutation analysis
D6V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  6(8Q11.21) MUTATED   3 5
  AMP PEAK  6(8Q11.21) WILD-TYPE 2 4
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                             8                              6 
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                             5                              4 
$`AMP PEAK  6(8Q11.21) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A264 
       10.26        45.70         6.31        12.99         6.58        31.33 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

$`AMP PEAK  6(8Q11.21) WILD-TYPE`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A1A1 TCGA-GN-A261 
       24.00         4.93        19.36        11.15        78.44        15.35 

  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                          6.31                           4.93 
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                         45.70                          78.44 
  AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE 
                        12.575                         17.355 
[1] "6.3 - 45.7 (12.6)" "4.9 - 78.4 (17.4)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK  6(8Q11.21) WILD-TYPE" "AMP PEAK  6(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK  6(8Q11.21) WILD-TYPE" "AMP PEAK  6(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK  6(8Q11.21) WILD-TYPE" "AMP PEAK  6(8Q11.21) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  6(8Q11.21) WILD-TYPE"   "AMP PEAK  6(8Q11.21) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  6(8Q11.21) MUTATED"   "AMP PEAK  6(8Q11.21) MUTATED" 
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK  6(8Q11.21) MUTATED                    2
  AMP PEAK  6(8Q11.21) WILD-TYPE                  1
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  6(8Q11.21) MUTATED                                                                                          3
  AMP PEAK  6(8Q11.21) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  6(8Q11.21) MUTATED                     7
  AMP PEAK  6(8Q11.21) WILD-TYPE                   7
D6V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  6(8Q11.21) MUTATED
  DISTANT METASTASIS                                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 7
                                                                                          clus
vv                                                                                         AMP PEAK  6(8Q11.21) WILD-TYPE
  DISTANT METASTASIS                                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                   7
D6V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q11.21) MUTATED      5    7
  AMP PEAK  6(8Q11.21) WILD-TYPE    7    4
        clus
vv       AMP PEAK  6(8Q11.21) MUTATED AMP PEAK  6(8Q11.21) WILD-TYPE
  FEMALE                            5                              7
  MALE                              7                              4
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK  6(8Q11.21) MUTATED    8  0   2   0   0  0
  AMP PEAK  6(8Q11.21) WILD-TYPE  3  1   0   3   2  2
D6V5, multiclass
D6V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  6(8Q11.21) MUTATED         2        0        1         2         3
  AMP PEAK  6(8Q11.21) WILD-TYPE       2        1        0         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(8Q11.21) MUTATED           0          2          0          0
  AMP PEAK  6(8Q11.21) WILD-TYPE         1          0          2          4
D6V7, multiclass

Clustering(7) Variable = Amp Peak  7(11q13.3) mutation analysis
D7V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  7(11Q13.3) MUTATED   2 2
  AMP PEAK  7(11Q13.3) WILD-TYPE 3 7
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                             4                             10 
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                             2                              7 
$`AMP PEAK  7(11Q13.3) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-ER-A3ET TCGA-GN-A26D 
       10.26        24.00         6.58        14.70 

$`AMP PEAK  7(11Q13.3) WILD-TYPE`
TCGA-D3-A3CC TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       45.70         4.93        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       78.44        15.35        31.33        12.16 

  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                          6.58                           4.93 
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                         24.00                          78.44 
  AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE 
                         12.48                          14.17 
[1] "6.6 - 24.0 (12.5)" "4.9 - 78.4 (14.2)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  7(11Q13.3) MUTATED" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  7(11Q13.3) WILD-TYPE" "AMP PEAK  7(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  7(11Q13.3) WILD-TYPE"   "AMP PEAK  7(11Q13.3) MUTATED" 
[1] "hr=" "1"  
D7V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK  7(11Q13.3) MUTATED                    1
  AMP PEAK  7(11Q13.3) WILD-TYPE                  2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  7(11Q13.3) MUTATED                                                                                          1
  AMP PEAK  7(11Q13.3) WILD-TYPE                                                                                        5
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  7(11Q13.3) MUTATED                     3
  AMP PEAK  7(11Q13.3) WILD-TYPE                  11
D7V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  7(11Q13.3) MUTATED
  DISTANT METASTASIS                                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 3
                                                                                          clus
vv                                                                                         AMP PEAK  7(11Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              5
  REGIONAL LYMPH NODE                                                                                                  11
D7V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11Q13.3) MUTATED      3    2
  AMP PEAK  7(11Q13.3) WILD-TYPE    9    9
        clus
vv       AMP PEAK  7(11Q13.3) MUTATED AMP PEAK  7(11Q13.3) WILD-TYPE
  FEMALE                            3                              9
  MALE                              2                              9
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK  7(11Q13.3) MUTATED    3  0   1   0   0  1
  AMP PEAK  7(11Q13.3) WILD-TYPE  8  1   1   3   2  1
D7V5, multiclass
D7V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  7(11Q13.3) MUTATED         0        0        1         1         1
  AMP PEAK  7(11Q13.3) WILD-TYPE       4        1        0         1         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(11Q13.3) MUTATED           0          1          0          1
  AMP PEAK  7(11Q13.3) WILD-TYPE         1          1          2          3
D7V7, multiclass

Clustering(8) Variable = Amp Peak  8(11q13.3) mutation analysis
D8V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  8(11Q13.3) MUTATED   2 2
  AMP PEAK  8(11Q13.3) WILD-TYPE 3 7
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                             4                             10 
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                             2                              7 
$`AMP PEAK  8(11Q13.3) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-ER-A3ET TCGA-GN-A26D 
       10.26        24.00         6.58        14.70 

$`AMP PEAK  8(11Q13.3) WILD-TYPE`
TCGA-D3-A3CC TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       45.70         4.93        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       78.44        15.35        31.33        12.16 

  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                          6.58                           4.93 
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                         24.00                          78.44 
  AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE 
                         12.48                          14.17 
[1] "6.6 - 24.0 (12.5)" "4.9 - 78.4 (14.2)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  8(11Q13.3) MUTATED" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  8(11Q13.3) WILD-TYPE" "AMP PEAK  8(11Q13.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK  8(11Q13.3) WILD-TYPE"   "AMP PEAK  8(11Q13.3) MUTATED" 
[1] "hr=" "1"  
D8V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK  8(11Q13.3) MUTATED                    1
  AMP PEAK  8(11Q13.3) WILD-TYPE                  2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  8(11Q13.3) MUTATED                                                                                          1
  AMP PEAK  8(11Q13.3) WILD-TYPE                                                                                        5
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  8(11Q13.3) MUTATED                     3
  AMP PEAK  8(11Q13.3) WILD-TYPE                  11
D8V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  8(11Q13.3) MUTATED
  DISTANT METASTASIS                                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 3
                                                                                          clus
vv                                                                                         AMP PEAK  8(11Q13.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              5
  REGIONAL LYMPH NODE                                                                                                  11
D8V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11Q13.3) MUTATED      3    2
  AMP PEAK  8(11Q13.3) WILD-TYPE    9    9
        clus
vv       AMP PEAK  8(11Q13.3) MUTATED AMP PEAK  8(11Q13.3) WILD-TYPE
  FEMALE                            3                              9
  MALE                              2                              9
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK  8(11Q13.3) MUTATED    3  0   1   0   0  1
  AMP PEAK  8(11Q13.3) WILD-TYPE  8  1   1   3   2  1
D8V5, multiclass
D8V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  8(11Q13.3) MUTATED         0        0        1         1         1
  AMP PEAK  8(11Q13.3) WILD-TYPE       4        1        0         1         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(11Q13.3) MUTATED           0          1          0          1
  AMP PEAK  8(11Q13.3) WILD-TYPE         1          1          2          3
D8V7, multiclass

Clustering(9) Variable = Amp Peak  9(12q14.1) mutation analysis
D9V1, survival
                                sevent
clus2                            0 1
  AMP PEAK  9(12Q14.1) MUTATED   3 6
  AMP PEAK  9(12Q14.1) WILD-TYPE 2 3
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                             9                              5 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                             6                              3 
$`AMP PEAK  9(12Q14.1) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A3ET 
       10.26        45.70        24.00         6.31        11.15         6.58 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        12.16        14.70 

$`AMP PEAK  9(12Q14.1) WILD-TYPE`
TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 
        4.93        19.36        12.99        78.44        15.35 

  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                          6.31                           4.93 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                         45.70                          78.44 
  AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE 
                         12.16                          15.35 
[1] "6.3 - 45.7 (12.2)" "4.9 - 78.4 (15.3)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK  9(12Q14.1) MUTATED" "AMP PEAK  9(12Q14.1) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK  9(12Q14.1) WILD-TYPE"   "AMP PEAK  9(12Q14.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK  9(12Q14.1) MUTATED"   "AMP PEAK  9(12Q14.1) MUTATED" 
[1] "hr=" "1.3"
D9V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK  9(12Q14.1) MUTATED                    1
  AMP PEAK  9(12Q14.1) WILD-TYPE                  2
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK  9(12Q14.1) MUTATED                                                                                          3
  AMP PEAK  9(12Q14.1) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK  9(12Q14.1) MUTATED                     6
  AMP PEAK  9(12Q14.1) WILD-TYPE                   8
D9V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK  9(12Q14.1) MUTATED
  DISTANT METASTASIS                                                                                                  1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 6
                                                                                          clus
vv                                                                                         AMP PEAK  9(12Q14.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                   8
D9V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q14.1) MUTATED      5    5
  AMP PEAK  9(12Q14.1) WILD-TYPE    7    6
        clus
vv       AMP PEAK  9(12Q14.1) MUTATED AMP PEAK  9(12Q14.1) WILD-TYPE
  FEMALE                            5                              7
  MALE                              5                              6
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK  9(12Q14.1) MUTATED    5  0   2   1   0  1
  AMP PEAK  9(12Q14.1) WILD-TYPE  6  1   0   2   2  1
D9V5, multiclass
D9V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK  9(12Q14.1) MUTATED         0        0        1         2         2
  AMP PEAK  9(12Q14.1) WILD-TYPE       4        1        0         0         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  9(12Q14.1) MUTATED           0          2          0          2
  AMP PEAK  9(12Q14.1) WILD-TYPE         1          0          2          2
D9V7, multiclass

Clustering(10) Variable = Amp Peak 10(17q25.3) mutation analysis
D10V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 10(17Q25.3) MUTATED   3 3
  AMP PEAK 10(17Q25.3) WILD-TYPE 2 6
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                             6                              8 
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                             3                              6 
$`AMP PEAK 10(17Q25.3) MUTATED`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A29D TCGA-ER-A3ET TCGA-GN-A26D 
       45.70        24.00         4.93        11.15         6.58        14.70 

$`AMP PEAK 10(17Q25.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 
       10.26        19.36         6.31        12.99        78.44        15.35 
TCGA-GN-A264 TCGA-GN-A26A 
       31.33        12.16 

  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                          4.93                           6.31 
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                         45.70                          78.44 
  AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE 
                        12.925                         14.170 
[1] "4.9 - 45.7 (12.9)" "6.3 - 78.4 (14.2)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK 10(17Q25.3) MUTATED"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK 10(17Q25.3) MUTATED" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK 10(17Q25.3) MUTATED"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK 10(17Q25.3) MUTATED" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
  "AMP PEAK 10(17Q25.3) MUTATED"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
  "AMP PEAK 10(17Q25.3) MUTATED" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 10(17Q25.3) WILD-TYPE" "AMP PEAK 10(17Q25.3) WILD-TYPE" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
"AMP PEAK 10(17Q25.3) WILD-TYPE"   "AMP PEAK 10(17Q25.3) MUTATED" 
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK 10(17Q25.3) MUTATED                    3
  AMP PEAK 10(17Q25.3) WILD-TYPE                  0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 10(17Q25.3) MUTATED                                                                                          2
  AMP PEAK 10(17Q25.3) WILD-TYPE                                                                                        4
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 10(17Q25.3) MUTATED                     5
  AMP PEAK 10(17Q25.3) WILD-TYPE                   9
D10V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 10(17Q25.3) MUTATED
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            2
  REGIONAL LYMPH NODE                                                                                                 5
                                                                                          clus
vv                                                                                         AMP PEAK 10(17Q25.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              4
  REGIONAL LYMPH NODE                                                                                                   9
D10V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(17Q25.3) MUTATED      6    4
  AMP PEAK 10(17Q25.3) WILD-TYPE    6    7
        clus
vv       AMP PEAK 10(17Q25.3) MUTATED AMP PEAK 10(17Q25.3) WILD-TYPE
  FEMALE                            6                              6
  MALE                              4                              7
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK 10(17Q25.3) MUTATED    6  0   1   2   0  1
  AMP PEAK 10(17Q25.3) WILD-TYPE  5  1   1   1   2  1
D10V5, multiclass
D10V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK 10(17Q25.3) MUTATED         1        1        1         0         3
  AMP PEAK 10(17Q25.3) WILD-TYPE       3        0        0         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(17Q25.3) MUTATED           0          1          1          2
  AMP PEAK 10(17Q25.3) WILD-TYPE         1          1          1          2
D10V7, multiclass

Clustering(11) Variable = Amp Peak 11(22q13.1) mutation analysis
D11V1, survival
                                sevent
clus2                            0 1
  AMP PEAK 11(22Q13.1) MUTATED   3 4
  AMP PEAK 11(22Q13.1) WILD-TYPE 2 5
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                             7                              7 
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                             4                              5 
$`AMP PEAK 11(22Q13.1) MUTATED`
TCGA-D3-A3CC TCGA-DA-A1IA TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26A 
       45.70         4.93        12.99         6.58        31.33        12.16 
TCGA-GN-A26D 
       14.70 

$`AMP PEAK 11(22Q13.1) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A1A1 
       10.26        24.00        19.36         6.31        11.15        78.44 
TCGA-GN-A261 
       15.35 

  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                          4.93                           6.31 
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                         45.70                          78.44 
  AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE 
                         12.99                          15.35 
[1] "4.9 - 45.7 (13.0)" "6.3 - 78.4 (15.3)"
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 11(22Q13.1) WILD-TYPE" "AMP PEAK 11(22Q13.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK 11(22Q13.1) MUTATED"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 11(22Q13.1) WILD-TYPE" "AMP PEAK 11(22Q13.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK 11(22Q13.1) MUTATED"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-D3-A2J6                     TCGA-D3-A3CC 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-D3-A3CF                     TCGA-DA-A1IA 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-DA-A3F2                     TCGA-EE-A17Z 
"AMP PEAK 11(22Q13.1) WILD-TYPE" "AMP PEAK 11(22Q13.1) WILD-TYPE" 
                    TCGA-EE-A29D                     TCGA-ER-A19L 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-ER-A1A1                     TCGA-ER-A3ET 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A261                     TCGA-GN-A264 
"AMP PEAK 11(22Q13.1) WILD-TYPE"   "AMP PEAK 11(22Q13.1) MUTATED" 
                    TCGA-GN-A26A                     TCGA-GN-A26D 
  "AMP PEAK 11(22Q13.1) MUTATED"   "AMP PEAK 11(22Q13.1) MUTATED" 
[1] "hr=" "1.2"
D11V2, continuous
                                vv
clus                             DISTANT METASTASIS
  AMP PEAK 11(22Q13.1) MUTATED                    3
  AMP PEAK 11(22Q13.1) WILD-TYPE                  0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 11(22Q13.1) MUTATED                                                                                          3
  AMP PEAK 11(22Q13.1) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  AMP PEAK 11(22Q13.1) MUTATED                     6
  AMP PEAK 11(22Q13.1) WILD-TYPE                   8
D11V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 11(22Q13.1) MUTATED
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 6
                                                                                          clus
vv                                                                                         AMP PEAK 11(22Q13.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                   8
D11V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(22Q13.1) MUTATED      7    5
  AMP PEAK 11(22Q13.1) WILD-TYPE    5    6
        clus
vv       AMP PEAK 11(22Q13.1) MUTATED AMP PEAK 11(22Q13.1) WILD-TYPE
  FEMALE                            7                              5
  MALE                              5                              6
                                vv
clus                             N0 N1 N1A N1B N2B N3
  AMP PEAK 11(22Q13.1) MUTATED    6  0   2   1   1  0
  AMP PEAK 11(22Q13.1) WILD-TYPE  5  1   0   2   1  2
D11V5, multiclass
D11V6, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK 11(22Q13.1) MUTATED         1        1        1         0         3
  AMP PEAK 11(22Q13.1) WILD-TYPE       3        0        0         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 11(22Q13.1) MUTATED           0          2          1          1
  AMP PEAK 11(22Q13.1) WILD-TYPE         1          0          1          3
D11V7, multiclass

Clustering(12) Variable = Amp Peak 12(Xq28) mutation analysis
D12V1, survival
                             sevent
clus2                         0 1
  AMP PEAK 12(XQ28) MUTATED   3 2
  AMP PEAK 12(XQ28) WILD-TYPE 2 7
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          5                           9 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          2                           7 
$`AMP PEAK 12(XQ28) MUTATED`
TCGA-D3-A3CC TCGA-EE-A29D TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26D 
       45.70        11.15         6.58        31.33        14.70 

$`AMP PEAK 12(XQ28) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        24.00         4.93        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A26A 
       78.44        15.35        12.16 

  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                       6.58                        4.93 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                      45.70                       78.44 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                      14.70                       12.99 
[1] "6.6 - 45.7 (14.7)" "4.9 - 78.4 (13.0)"
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK 12(XQ28) MUTATED" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK 12(XQ28) MUTATED" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"AMP PEAK 12(XQ28) WILD-TYPE" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
  "AMP PEAK 12(XQ28) MUTATED" "AMP PEAK 12(XQ28) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"AMP PEAK 12(XQ28) WILD-TYPE"   "AMP PEAK 12(XQ28) MUTATED" 
[1] "hr=" "2.6"
D12V2, continuous
                             vv
clus                          DISTANT METASTASIS
  AMP PEAK 12(XQ28) MUTATED                    2
  AMP PEAK 12(XQ28) WILD-TYPE                  1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 12(XQ28) MUTATED                                                                                          2
  AMP PEAK 12(XQ28) WILD-TYPE                                                                                        4
                             vv
clus                          REGIONAL LYMPH NODE
  AMP PEAK 12(XQ28) MUTATED                     4
  AMP PEAK 12(XQ28) WILD-TYPE                  10
D12V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 12(XQ28) MUTATED
  DISTANT METASTASIS                                                                                               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         2
  REGIONAL LYMPH NODE                                                                                              4
                                                                                          clus
vv                                                                                         AMP PEAK 12(XQ28) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                               10
D12V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      5    3
  AMP PEAK 12(XQ28) WILD-TYPE    7    8
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  FEMALE                         5                           7
  MALE                           3                           8
                             vv
clus                          N0 N1 N1A N1B N2B N3
  AMP PEAK 12(XQ28) MUTATED    4  0   1   1   1  0
  AMP PEAK 12(XQ28) WILD-TYPE  7  1   1   2   1  2
D12V5, multiclass
D12V6, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  AMP PEAK 12(XQ28) MUTATED         0        0        1         0         3
  AMP PEAK 12(XQ28) WILD-TYPE       4        1        0         2         0
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(XQ28) MUTATED           0          1          0          2
  AMP PEAK 12(XQ28) WILD-TYPE         1          1          2          2
D12V7, multiclass

Clustering(13) Variable = Del Peak 1(2q37.3) mutation analysis
D13V1, survival
                              sevent
clus2                          0 1
  DEL PEAK 1(2Q37.3) MUTATED   2 3
  DEL PEAK 1(2Q37.3) WILD-TYPE 3 6
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                           5                            9 
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                           3                            6 
$`DEL PEAK 1(2Q37.3) MUTATED`
TCGA-DA-A1IA TCGA-EE-A29D TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26D 
        4.93        11.15         6.58        31.33        14.70 

$`DEL PEAK 1(2Q37.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        45.70        24.00        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A26A 
       78.44        15.35        12.16 

  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                        4.93                         6.31 
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                       31.33                        78.44 
  DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE 
                       11.15                        15.35 
[1] "4.9 - 31.3 (11.2)" "6.3 - 78.4 (15.3)"
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 1(2Q37.3) MUTATED" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 1(2Q37.3) MUTATED" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 1(2Q37.3) WILD-TYPE" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 1(2Q37.3) MUTATED" "DEL PEAK 1(2Q37.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 1(2Q37.3) WILD-TYPE"   "DEL PEAK 1(2Q37.3) MUTATED" 
[1] "hr=" "1.3"
D13V2, continuous
                              vv
clus                           DISTANT METASTASIS
  DEL PEAK 1(2Q37.3) MUTATED                    1
  DEL PEAK 1(2Q37.3) WILD-TYPE                  2
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 1(2Q37.3) MUTATED                                                                                          2
  DEL PEAK 1(2Q37.3) WILD-TYPE                                                                                        4
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 1(2Q37.3) MUTATED                     4
  DEL PEAK 1(2Q37.3) WILD-TYPE                  10
D13V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 1(2Q37.3) MUTATED
  DISTANT METASTASIS                                                                                                1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          2
  REGIONAL LYMPH NODE                                                                                               4
                                                                                          clus
vv                                                                                         DEL PEAK 1(2Q37.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            4
  REGIONAL LYMPH NODE                                                                                                10
D13V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 1(2Q37.3) MUTATED      5    2
  DEL PEAK 1(2Q37.3) WILD-TYPE    7    9
        clus
vv       DEL PEAK 1(2Q37.3) MUTATED DEL PEAK 1(2Q37.3) WILD-TYPE
  FEMALE                          5                            7
  MALE                            2                            9
                              vv
clus                           N0 N1 N1A N1B N2B N3
  DEL PEAK 1(2Q37.3) MUTATED    2  0   1   3   0  0
  DEL PEAK 1(2Q37.3) WILD-TYPE  9  1   1   0   2  2
D13V5, multiclass
D13V6, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 1(2Q37.3) MUTATED         1        0        0         0         1
  DEL PEAK 1(2Q37.3) WILD-TYPE       3        1        1         2         2
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 1(2Q37.3) MUTATED           0          1          1          1
  DEL PEAK 1(2Q37.3) WILD-TYPE         1          1          1          3
D13V7, multiclass

Clustering(14) Variable = Del Peak 2(4q34.3) mutation analysis
D14V1, survival
                              sevent
clus2                          0 1
  DEL PEAK 2(4Q34.3) MUTATED   2 0
  DEL PEAK 2(4Q34.3) WILD-TYPE 3 9
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           2                           12 
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           0                            9 
$`DEL PEAK 2(4Q34.3) MUTATED`
TCGA-D3-A3CC TCGA-ER-A3ET 
       45.70         6.58 

$`DEL PEAK 2(4Q34.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99        78.44        15.35        31.33        12.16        14.70 

  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                        6.58                         4.93 
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                       45.70                        78.44 
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                      26.140                       13.845 
[1] "6.6 - 45.7 (26.1)" "4.9 - 78.4 (13.8)"
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 2(4Q34.3) WILD-TYPE"   "DEL PEAK 2(4Q34.3) MUTATED" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
[1] "Remove cluster labels:"     "DEL PEAK 2(4Q34.3) MUTATED"
clus
  DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE 
                           2                           12 
                  TCGA-D3-A2J6                   TCGA-D3-A3CF 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-DA-A1IA                   TCGA-DA-A3F2 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-EE-A17Z                   TCGA-EE-A29D 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-ER-A19L                   TCGA-ER-A1A1 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
"DEL PEAK 2(4Q34.3) WILD-TYPE" "DEL PEAK 2(4Q34.3) WILD-TYPE" 
D14V2, continuous
                              vv
clus                           DISTANT METASTASIS
  DEL PEAK 2(4Q34.3) MUTATED                    0
  DEL PEAK 2(4Q34.3) WILD-TYPE                  3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 2(4Q34.3) MUTATED                                                                                          3
  DEL PEAK 2(4Q34.3) WILD-TYPE                                                                                        3
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 2(4Q34.3) MUTATED                     4
  DEL PEAK 2(4Q34.3) WILD-TYPE                  10
D14V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 2(4Q34.3) MUTATED
  DISTANT METASTASIS                                                                                                0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          3
  REGIONAL LYMPH NODE                                                                                               4
                                                                                          clus
vv                                                                                         DEL PEAK 2(4Q34.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                10
D14V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 2(4Q34.3) MUTATED      5    2
  DEL PEAK 2(4Q34.3) WILD-TYPE    7    9
        clus
vv       DEL PEAK 2(4Q34.3) MUTATED DEL PEAK 2(4Q34.3) WILD-TYPE
  FEMALE                          5                            7
  MALE                            2                            9
                              vv
clus                           N0 N1 N1A N1B N2B N3
  DEL PEAK 2(4Q34.3) MUTATED    4  0   1   1   1  0
  DEL PEAK 2(4Q34.3) WILD-TYPE  7  1   1   2   1  2
D14V5, multiclass
D14V6, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 2(4Q34.3) MUTATED         2        1        0         0         1
  DEL PEAK 2(4Q34.3) WILD-TYPE       2        0        1         2         2
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 2(4Q34.3) MUTATED           0          1          0          1
  DEL PEAK 2(4Q34.3) WILD-TYPE         1          1          2          3
D14V7, multiclass

Clustering(15) Variable = Del Peak 3(5p15.31) mutation analysis
D15V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 3(5P15.31) MUTATED   2 2
  DEL PEAK 3(5P15.31) WILD-TYPE 3 7
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            4                            10 
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                            2                             7 
$`DEL PEAK 3(5P15.31) MUTATED`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-GN-A264 TCGA-GN-A26D 
       45.70        24.00        31.33        14.70 

$`DEL PEAK 3(5P15.31) WILD-TYPE`
TCGA-D3-A2J6 TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       10.26         4.93        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A 
       78.44         6.58        15.35        12.16 

  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                        14.70                          4.93 
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                        45.70                         78.44 
  DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE 
                       27.665                        11.655 
[1] "14.7 - 45.7 (27.7)" "4.9 - 78.4 (11.7)" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 3(5P15.31) MUTATED" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 3(5P15.31) MUTATED" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 3(5P15.31) MUTATED" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 3(5P15.31) WILD-TYPE" "DEL PEAK 3(5P15.31) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 3(5P15.31) WILD-TYPE"   "DEL PEAK 3(5P15.31) MUTATED" 
[1] "hr=" "3.4"
D15V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK 3(5P15.31) MUTATED                    0
  DEL PEAK 3(5P15.31) WILD-TYPE                  3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 3(5P15.31) MUTATED                                                                                          1
  DEL PEAK 3(5P15.31) WILD-TYPE                                                                                        5
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 3(5P15.31) MUTATED                     4
  DEL PEAK 3(5P15.31) WILD-TYPE                  10
D15V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 3(5P15.31) MUTATED
  DISTANT METASTASIS                                                                                                 0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                                4
                                                                                          clus
vv                                                                                         DEL PEAK 3(5P15.31) WILD-TYPE
  DISTANT METASTASIS                                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             5
  REGIONAL LYMPH NODE                                                                                                 10
D15V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 3(5P15.31) MUTATED      3    2
  DEL PEAK 3(5P15.31) WILD-TYPE    9    9
        clus
vv       DEL PEAK 3(5P15.31) MUTATED DEL PEAK 3(5P15.31) WILD-TYPE
  FEMALE                           3                             9
  MALE                             2                             9
                               vv
clus                            N0 N1 N1A N1B N2B N3
  DEL PEAK 3(5P15.31) MUTATED    3  0   0   0   0  1
  DEL PEAK 3(5P15.31) WILD-TYPE  8  1   2   3   2  1
D15V5, multiclass
D15V6, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 3(5P15.31) MUTATED         0        1        0         0         2
  DEL PEAK 3(5P15.31) WILD-TYPE       4        0        1         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 3(5P15.31) MUTATED           0          0          0          1
  DEL PEAK 3(5P15.31) WILD-TYPE         1          2          2          3
D15V7, multiclass

Clustering(16) Variable = Del Peak 4(9p21.3) mutation analysis
D16V1, survival
                              sevent
clus2                          0 1
  DEL PEAK 4(9P21.3) MUTATED   2 7
  DEL PEAK 4(9P21.3) WILD-TYPE 3 2
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                           9                            5 
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                           7                            2 
$`DEL PEAK 4(9P21.3) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A29D TCGA-ER-A19L 
       10.26        45.70        24.00         4.93        11.15        12.99 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        12.16        14.70 

$`DEL PEAK 4(9P21.3) WILD-TYPE`
TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       19.36         6.31        78.44         6.58        15.35 

  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                        4.93                         6.31 
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                       45.70                        78.44 
  DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE 
                       12.99                        15.35 
[1] "4.9 - 45.7 (13.0)" "6.3 - 78.4 (15.3)"
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 4(9P21.3) WILD-TYPE"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 4(9P21.3) WILD-TYPE"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-D3-A2J6                   TCGA-D3-A3CC 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-D3-A3CF                   TCGA-DA-A1IA 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-DA-A3F2                   TCGA-EE-A17Z 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-EE-A29D                   TCGA-ER-A19L 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-ER-A1A1                   TCGA-ER-A3ET 
"DEL PEAK 4(9P21.3) WILD-TYPE" "DEL PEAK 4(9P21.3) WILD-TYPE" 
                  TCGA-GN-A261                   TCGA-GN-A264 
"DEL PEAK 4(9P21.3) WILD-TYPE"   "DEL PEAK 4(9P21.3) MUTATED" 
                  TCGA-GN-A26A                   TCGA-GN-A26D 
  "DEL PEAK 4(9P21.3) MUTATED"   "DEL PEAK 4(9P21.3) MUTATED" 
[1] "hr=" "1.9"
D16V2, continuous
                              vv
clus                           DISTANT METASTASIS
  DEL PEAK 4(9P21.3) MUTATED                    1
  DEL PEAK 4(9P21.3) WILD-TYPE                  2
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 4(9P21.3) MUTATED                                                                                          3
  DEL PEAK 4(9P21.3) WILD-TYPE                                                                                        3
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 4(9P21.3) MUTATED                    10
  DEL PEAK 4(9P21.3) WILD-TYPE                   4
D16V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 4(9P21.3) MUTATED
  DISTANT METASTASIS                                                                                                1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          3
  REGIONAL LYMPH NODE                                                                                              10
                                                                                          clus
vv                                                                                         DEL PEAK 4(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 4
D16V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 4(9P21.3) MUTATED      8    6
  DEL PEAK 4(9P21.3) WILD-TYPE    4    5
        clus
vv       DEL PEAK 4(9P21.3) MUTATED DEL PEAK 4(9P21.3) WILD-TYPE
  FEMALE                          8                            4
  MALE                            6                            5
                              vv
clus                           N0 N1 N1A N1B N2B N3
  DEL PEAK 4(9P21.3) MUTATED    6  0   1   3   1  1
  DEL PEAK 4(9P21.3) WILD-TYPE  5  1   1   0   1  1
D16V5, multiclass
D16V6, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 4(9P21.3) MUTATED         2        1        0         1         2
  DEL PEAK 4(9P21.3) WILD-TYPE       2        0        1         1         1
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 4(9P21.3) MUTATED           0          1          1          3
  DEL PEAK 4(9P21.3) WILD-TYPE         1          1          1          1
D16V7, multiclass

Clustering(17) Variable = Del Peak 5(10q26.3) mutation analysis
D17V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 5(10Q26.3) MUTATED   2 7
  DEL PEAK 5(10Q26.3) WILD-TYPE 3 2
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                            9                             5 
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                            7                             2 
$`DEL PEAK 5(10Q26.3) MUTATED`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       45.70        24.00         4.93         6.31        11.15        12.99 
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26A 
        6.58        31.33        12.16 

$`DEL PEAK 5(10Q26.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-DA-A3F2 TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A26D 
       10.26        19.36        78.44        15.35        14.70 

  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                         4.93                         10.26 
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                        45.70                         78.44 
  DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE 
                        12.16                         15.35 
[1] "4.9 - 45.7 (12.2)"  "10.3 - 78.4 (15.3)"
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 5(10Q26.3) MUTATED" "DEL PEAK 5(10Q26.3) WILD-TYPE" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 5(10Q26.3) MUTATED" "DEL PEAK 5(10Q26.3) WILD-TYPE" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 5(10Q26.3) MUTATED"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 5(10Q26.3) WILD-TYPE"   "DEL PEAK 5(10Q26.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 5(10Q26.3) MUTATED" "DEL PEAK 5(10Q26.3) WILD-TYPE" 
[1] "hr=" "2.4"
D17V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK 5(10Q26.3) MUTATED                    2
  DEL PEAK 5(10Q26.3) WILD-TYPE                  1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 5(10Q26.3) MUTATED                                                                                          4
  DEL PEAK 5(10Q26.3) WILD-TYPE                                                                                        2
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 5(10Q26.3) MUTATED                     7
  DEL PEAK 5(10Q26.3) WILD-TYPE                   7
D17V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 5(10Q26.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                7
                                                                                          clus
vv                                                                                         DEL PEAK 5(10Q26.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
  REGIONAL LYMPH NODE                                                                                                  7
D17V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 5(10Q26.3) MUTATED      8    5
  DEL PEAK 5(10Q26.3) WILD-TYPE    4    6
        clus
vv       DEL PEAK 5(10Q26.3) MUTATED DEL PEAK 5(10Q26.3) WILD-TYPE
  FEMALE                           8                             4
  MALE                             5                             6
                               vv
clus                            N0 N1 N1A N1B N2B N3
  DEL PEAK 5(10Q26.3) MUTATED    5  0   2   3   0  1
  DEL PEAK 5(10Q26.3) WILD-TYPE  6  1   0   0   2  1
D17V5, multiclass
D17V6, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 5(10Q26.3) MUTATED         1        1        0         1         2
  DEL PEAK 5(10Q26.3) WILD-TYPE       3        0        1         1         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 5(10Q26.3) MUTATED           0          2          1          2
  DEL PEAK 5(10Q26.3) WILD-TYPE         1          0          1          2
D17V7, multiclass

Clustering(18) Variable = Del Peak 6(11q23.3) mutation analysis
D18V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 6(11Q23.3) MUTATED   3 7
  DEL PEAK 6(11Q23.3) WILD-TYPE 2 2
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                           10                             4 
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                            7                             2 
$`DEL PEAK 6(11Q23.3) MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A29D TCGA-ER-A19L 
       10.26        45.70        24.00         4.93        11.15        12.99 
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        6.58        31.33        12.16        14.70 

$`DEL PEAK 6(11Q23.3) WILD-TYPE`
TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 TCGA-GN-A261 
       19.36         6.31        78.44        15.35 

  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                         4.93                          6.31 
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                        45.70                         78.44 
  DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE 
                       12.575                        17.355 
[1] "4.9 - 45.7 (12.6)" "6.3 - 78.4 (17.4)"
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 6(11Q23.3) WILD-TYPE" "DEL PEAK 6(11Q23.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 6(11Q23.3) WILD-TYPE" "DEL PEAK 6(11Q23.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 6(11Q23.3) WILD-TYPE" "DEL PEAK 6(11Q23.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 6(11Q23.3) WILD-TYPE"   "DEL PEAK 6(11Q23.3) MUTATED" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
  "DEL PEAK 6(11Q23.3) MUTATED"   "DEL PEAK 6(11Q23.3) MUTATED" 
[1] "hr=" "1.7"
D18V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK 6(11Q23.3) MUTATED                    2
  DEL PEAK 6(11Q23.3) WILD-TYPE                  1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 6(11Q23.3) MUTATED                                                                                          4
  DEL PEAK 6(11Q23.3) WILD-TYPE                                                                                        2
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 6(11Q23.3) MUTATED                     8
  DEL PEAK 6(11Q23.3) WILD-TYPE                   6
D18V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 6(11Q23.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                8
                                                                                          clus
vv                                                                                         DEL PEAK 6(11Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
  REGIONAL LYMPH NODE                                                                                                  6
D18V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 6(11Q23.3) MUTATED      9    5
  DEL PEAK 6(11Q23.3) WILD-TYPE    3    6
        clus
vv       DEL PEAK 6(11Q23.3) MUTATED DEL PEAK 6(11Q23.3) WILD-TYPE
  FEMALE                           9                             3
  MALE                             5                             6
                               vv
clus                            N0 N1 N1A N1B N2B N3
  DEL PEAK 6(11Q23.3) MUTATED    6  0   2   3   0  1
  DEL PEAK 6(11Q23.3) WILD-TYPE  5  1   0   0   2  1
D18V5, multiclass
D18V6, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 6(11Q23.3) MUTATED         1        1        0         1         3
  DEL PEAK 6(11Q23.3) WILD-TYPE       3        0        1         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 6(11Q23.3) MUTATED           0          2          1          2
  DEL PEAK 6(11Q23.3) WILD-TYPE         1          0          1          2
D18V7, multiclass

Clustering(19) Variable = Del Peak 7(15q14) mutation analysis
D19V1, survival
                             sevent
clus2                         0 1
  DEL PEAK 7(15Q14) MUTATED   3 2
  DEL PEAK 7(15Q14) WILD-TYPE 2 7
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                          5                           9 
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                          2                           7 
$`DEL PEAK 7(15Q14) MUTATED`
TCGA-D3-A3CC TCGA-DA-A1IA TCGA-EE-A17Z TCGA-ER-A3ET TCGA-GN-A26D 
       45.70         4.93         6.31         6.58        14.70 

$`DEL PEAK 7(15Q14) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A19L TCGA-ER-A1A1 
       10.26        24.00        19.36        11.15        12.99        78.44 
TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       15.35        31.33        12.16 

  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                       4.93                       10.26 
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                      45.70                       78.44 
  DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE 
                       6.58                       15.35 
[1] "4.9 - 45.7 (6.6)"   "10.3 - 78.4 (15.3)"
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-D3-A2J6                  TCGA-D3-A3CC 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-D3-A3CF                  TCGA-DA-A1IA 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-DA-A3F2                  TCGA-EE-A17Z 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-EE-A29D                  TCGA-ER-A19L 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-ER-A1A1                  TCGA-ER-A3ET 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
                 TCGA-GN-A261                  TCGA-GN-A264 
"DEL PEAK 7(15Q14) WILD-TYPE" "DEL PEAK 7(15Q14) WILD-TYPE" 
                 TCGA-GN-A26A                  TCGA-GN-A26D 
"DEL PEAK 7(15Q14) WILD-TYPE"   "DEL PEAK 7(15Q14) MUTATED" 
[1] "hr=" "1.2"
D19V2, continuous
                             vv
clus                          DISTANT METASTASIS
  DEL PEAK 7(15Q14) MUTATED                    2
  DEL PEAK 7(15Q14) WILD-TYPE                  1
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 7(15Q14) MUTATED                                                                                          2
  DEL PEAK 7(15Q14) WILD-TYPE                                                                                        4
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK 7(15Q14) MUTATED                     5
  DEL PEAK 7(15Q14) WILD-TYPE                   9
D19V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 7(15Q14) MUTATED
  DISTANT METASTASIS                                                                                               2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         2
  REGIONAL LYMPH NODE                                                                                              5
                                                                                          clus
vv                                                                                         DEL PEAK 7(15Q14) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                9
D19V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 7(15Q14) MUTATED      6    3
  DEL PEAK 7(15Q14) WILD-TYPE    6    8
        clus
vv       DEL PEAK 7(15Q14) MUTATED DEL PEAK 7(15Q14) WILD-TYPE
  FEMALE                         6                           6
  MALE                           3                           8
                             vv
clus                          N0 N1 N1A N1B N2B N3
  DEL PEAK 7(15Q14) MUTATED    6  0   1   1   1  0
  DEL PEAK 7(15Q14) WILD-TYPE  5  1   1   2   1  2
D19V5, multiclass
D19V6, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 7(15Q14) MUTATED         2        0        1         1         2
  DEL PEAK 7(15Q14) WILD-TYPE       2        1        0         1         1
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 7(15Q14) MUTATED           0          1          1          1
  DEL PEAK 7(15Q14) WILD-TYPE         1          1          1          3
D19V7, multiclass

Clustering(20) Variable = Del Peak 8(16p13.3) mutation analysis
D20V1, survival
                               sevent
clus2                           0 1
  DEL PEAK 8(16P13.3) MUTATED   2 1
  DEL PEAK 8(16P13.3) WILD-TYPE 3 8
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            3                            11 
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                            1                             8 
$`DEL PEAK 8(16P13.3) MUTATED`
TCGA-D3-A3CC TCGA-EE-A29D TCGA-GN-A26D 
       45.70        11.15        14.70 

$`DEL PEAK 8(16P13.3) WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        24.00         4.93        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       78.44         6.58        15.35        31.33        12.16 

  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                        11.15                          4.93 
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                        45.70                         78.44 
  DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE 
                        14.70                         12.99 
[1] "11.2 - 45.7 (14.7)" "4.9 - 78.4 (13.0)" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 8(16P13.3) MUTATED" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 8(16P13.3) MUTATED" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
                   TCGA-D3-A2J6                    TCGA-D3-A3CC 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
                   TCGA-D3-A3CF                    TCGA-DA-A1IA 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-DA-A3F2                    TCGA-EE-A17Z 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-EE-A29D                    TCGA-ER-A19L 
  "DEL PEAK 8(16P13.3) MUTATED" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-ER-A1A1                    TCGA-ER-A3ET 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A261                    TCGA-GN-A264 
"DEL PEAK 8(16P13.3) WILD-TYPE" "DEL PEAK 8(16P13.3) WILD-TYPE" 
                   TCGA-GN-A26A                    TCGA-GN-A26D 
"DEL PEAK 8(16P13.3) WILD-TYPE"   "DEL PEAK 8(16P13.3) MUTATED" 
[1] "hr=" "2.7"
D20V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK 8(16P13.3) MUTATED                    1
  DEL PEAK 8(16P13.3) WILD-TYPE                  2
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 8(16P13.3) MUTATED                                                                                          1
  DEL PEAK 8(16P13.3) WILD-TYPE                                                                                        5
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK 8(16P13.3) MUTATED                     2
  DEL PEAK 8(16P13.3) WILD-TYPE                  12
D20V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 8(16P13.3) MUTATED
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                                2
                                                                                          clus
vv                                                                                         DEL PEAK 8(16P13.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             5
  REGIONAL LYMPH NODE                                                                                                 12
D20V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 8(16P13.3) MUTATED      3    1
  DEL PEAK 8(16P13.3) WILD-TYPE    9   10
        clus
vv       DEL PEAK 8(16P13.3) MUTATED DEL PEAK 8(16P13.3) WILD-TYPE
  FEMALE                           3                             9
  MALE                             1                            10
                               vv
clus                            N0 N1 N1A N1B N2B N3
  DEL PEAK 8(16P13.3) MUTATED    3  0   0   1   0  0
  DEL PEAK 8(16P13.3) WILD-TYPE  8  1   2   2   2  2
D20V5, multiclass
D20V6, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC
  DEL PEAK 8(16P13.3) MUTATED         0        0        0         0         3
  DEL PEAK 8(16P13.3) WILD-TYPE       4        1        1         2         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 8(16P13.3) MUTATED           0          0          0          1
  DEL PEAK 8(16P13.3) WILD-TYPE         1          2          2          3
D20V7, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"   "LYMPH.NODE.METASTASIS"         "TUMOR.STAGECODE" 
                       V7 
  "NEOPLASM.DISEASESTAGE" 
> q(save="no")
