
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/404227/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NF1_Any_Mutants/3215659/SKCM-NF1_Any_Mutants.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-NF1_Any_Mutants", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                      "-oT=SKCM-NF1_Any_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=25, in cluster file=31, common to both=25
[1] 19 25
[1] "Amp Peak 1(1p12) mutation analysis"
[1] 3
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                         8                         17 
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                         8                         17 
[1] "Amp Peak 2(1q44) mutation analysis"
[1] 3
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        17                          8 
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        17                          8 
[1] "Amp Peak 3(7p22.3) mutation analysis"
[1] 3
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          14                           11 
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          14                           11 
[1] "Amp Peak 4(7q36.1) mutation analysis"
[1] 3
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          14                           11 
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          14                           11 
[1] "Amp Peak 5(12p12.1) mutation analysis"
[1] 3
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            3                            22 
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            3                            22 
[1] "Amp Peak 6(15q26.2) mutation analysis"
[1] 3
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                            8                            17 
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                            8                            17 
[1] "Amp Peak 7(17q25.3) mutation analysis"
[1] 3
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                           15                            10 
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                           15                            10 
[1] "Del Peak  1(1p36.31) mutation analysis"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             6                             19 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             6                             19 
[1] "Del Peak  2(1p13.2) mutation analysis"
[1] 3
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                            16 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                            16 
[1] "Del Peak  3(2q37.3) mutation analysis"
[1] 3
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            8                            17 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            8                            17 
[1] "Del Peak  4(3q23) mutation analysis"
[1] 3
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          3                          22 
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          3                          22 
[1] "Del Peak  5(6q23.2) mutation analysis"
[1] 3
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                           14                            11 
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                           14                            11 
[1] "Del Peak  6(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           19                             6 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           19                             6 
[1] "Del Peak  7(10p15.1) mutation analysis"
[1] 3
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                            11                             14 
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                            11                             14 
[1] "Del Peak  8(10q24.33) mutation analysis"
[1] 3
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                             12                              13 
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                             12                              13 
[1] "Del Peak  9(11q24.3) mutation analysis"
[1] 3
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            19                              6 
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            19                              6 
[1] "Del Peak 10(13q34) mutation analysis"
[1] 3
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           7                           18 
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           7                           18 
[1] "Del Peak 11(14q23.3) mutation analysis"
[1] 3
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             6                             19 
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             6                             19 
[1] "Del Peak 12(16q12.1) mutation analysis"
[1] 3
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                            12                             13 
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                            12                             13 
[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 25 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        1483           NA           NA           NA           NA           NA 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO 
          NA           NA           NA          743         1315         3101 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
         435           NA           NA         4150         1265          813 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
          NA           NA           NA           NA           NA            6 
TCGA-GN-A266 
          NA 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=12,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T1A T2A  T3 T3A T3B  T4 T4B  TX 
  3   1   2   2   4   2   7   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 25 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, 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=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(1p12) mutation analysis
D1V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 1(1P12) MUTATED    2  6
  AMP PEAK 1(1P12) WILD-TYPE  7 10
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                         8                         17 
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                         6                         10 
$`AMP PEAK 1(1P12) MUTATED`
TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       33.73         2.56        25.87        14.30       204.62        96.23 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$`AMP PEAK 1(1P12) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N 
       48.76        20.38        68.09        29.82        14.70        18.58 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       24.43        43.23       101.95       136.44        41.59        26.73 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       26.37        20.91        27.68        74.73        27.02 

  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                       0.2                       14.7 
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                    204.62                     136.44 
  AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE 
                    20.085                     27.680 
[1] "0.2 - 204.6 (20.1)"  "14.7 - 136.4 (27.7)"
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
  "AMP PEAK 1(1P12) MUTATED"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
"AMP PEAK 1(1P12) WILD-TYPE"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 1(1P12) MUTATED" 
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
  "AMP PEAK 1(1P12) MUTATED"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
"AMP PEAK 1(1P12) WILD-TYPE"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 1(1P12) MUTATED" 
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
  "AMP PEAK 1(1P12) MUTATED"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 1(1P12) MUTATED" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
"AMP PEAK 1(1P12) WILD-TYPE" "AMP PEAK 1(1P12) WILD-TYPE" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
"AMP PEAK 1(1P12) WILD-TYPE"   "AMP PEAK 1(1P12) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 1(1P12) MUTATED" 
[1] "hr=" "1.3"
D1V2, continuous
                            vv
clus                         DISTANT METASTASIS
  AMP PEAK 1(1P12) MUTATED                    2
  AMP PEAK 1(1P12) WILD-TYPE                  5
                            vv
clus                         REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 1(1P12) MUTATED                                                                                          2
  AMP PEAK 1(1P12) WILD-TYPE                                                                                        3
                            vv
clus                         REGIONAL LYMPH NODE
  AMP PEAK 1(1P12) MUTATED                     4
  AMP PEAK 1(1P12) WILD-TYPE                   9
D1V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 1(1P12) MUTATED
  DISTANT METASTASIS                                                                                              2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                        2
  REGIONAL LYMPH NODE                                                                                             4
                                                                                          clus
vv                                                                                         AMP PEAK 1(1P12) WILD-TYPE
  DISTANT METASTASIS                                                                                                5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          3
  REGIONAL LYMPH NODE                                                                                               9
D1V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1P12) MUTATED      2    6
  AMP PEAK 1(1P12) WILD-TYPE    6   11
        clus
vv       AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  FEMALE                        2                          6
  MALE                          6                         11
                            vv
clus                         N0 N1B N2C N3
  AMP PEAK 1(1P12) MUTATED    5   1   0  1
  AMP PEAK 1(1P12) WILD-TYPE 11   2   2  1
D1V5, multiclass
     clus
vv    AMP PEAK 1(1P12) MUTATED AMP PEAK 1(1P12) WILD-TYPE
  N0                         5                         11
  N1B                        1                          2
  N2C                        0                          2
  N3                         1                          1
D1V6, continuous
                            vv
clus                         STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 1(1P12) MUTATED          0        0        3         1          0
  AMP PEAK 1(1P12) WILD-TYPE        3        1        3         2          3
                            vv
clus                         STAGE IIIC STAGE IV
  AMP PEAK 1(1P12) MUTATED            2        1
  AMP PEAK 1(1P12) WILD-TYPE          2        0
D1V7, multiclass

Clustering(2) Variable = Amp Peak 2(1q44) mutation analysis
D2V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 2(1Q44) MUTATED    5 12
  AMP PEAK 2(1Q44) WILD-TYPE  4  4
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        17                          8 
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                        12                          4 
$`AMP PEAK 2(1Q44) MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 
       20.38        68.09        33.73        14.70         2.56        24.43 
TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 
      101.95        96.23       136.44        41.59        26.37        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.68        74.73        27.02         0.20        10.09 

$`AMP PEAK 2(1Q44) WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GR 
       48.76        29.82        18.58        25.87        43.23        14.30 
TCGA-EE-A2MI TCGA-EE-A3AE 
      204.62        26.73 

  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                       0.2                       14.3 
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                    136.44                     204.62 
  AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE 
                    27.020                     28.275 
[1] "0.2 - 136.4 (27.0)"  "14.3 - 204.6 (28.3)"
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
"AMP PEAK 2(1Q44) WILD-TYPE" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
"AMP PEAK 2(1Q44) WILD-TYPE" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-D3-A2JF                 TCGA-DA-A1I0 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-DA-A1IC                 TCGA-EE-A17X 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A181                 TCGA-EE-A182 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A29L                 TCGA-EE-A29N 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A29V                 TCGA-EE-A2A2 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GC                 TCGA-EE-A2GO 
"AMP PEAK 2(1Q44) WILD-TYPE"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2GR                 TCGA-EE-A2MI 
"AMP PEAK 2(1Q44) WILD-TYPE" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-EE-A2MJ                 TCGA-EE-A2MS 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-EE-A2MT                 TCGA-EE-A3AE 
  "AMP PEAK 2(1Q44) MUTATED" "AMP PEAK 2(1Q44) WILD-TYPE" 
                TCGA-ER-A19F                 TCGA-FS-A1Z3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZA                 TCGA-FS-A1ZP 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-FS-A1ZZ                 TCGA-FW-A3I3 
  "AMP PEAK 2(1Q44) MUTATED"   "AMP PEAK 2(1Q44) MUTATED" 
                TCGA-GN-A266 
  "AMP PEAK 2(1Q44) MUTATED" 
[1] "hr=" "1.8"
D2V2, continuous
                            vv
clus                         DISTANT METASTASIS
  AMP PEAK 2(1Q44) MUTATED                    5
  AMP PEAK 2(1Q44) WILD-TYPE                  2
                            vv
clus                         REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 2(1Q44) MUTATED                                                                                          4
  AMP PEAK 2(1Q44) WILD-TYPE                                                                                        1
                            vv
clus                         REGIONAL LYMPH NODE
  AMP PEAK 2(1Q44) MUTATED                     8
  AMP PEAK 2(1Q44) WILD-TYPE                   5
D2V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 2(1Q44) MUTATED
  DISTANT METASTASIS                                                                                              5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                        4
  REGIONAL LYMPH NODE                                                                                             8
                                                                                          clus
vv                                                                                         AMP PEAK 2(1Q44) WILD-TYPE
  DISTANT METASTASIS                                                                                                2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          1
  REGIONAL LYMPH NODE                                                                                               5
D2V4, binary
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(1Q44) MUTATED      7   10
  AMP PEAK 2(1Q44) WILD-TYPE    1    7
        clus
vv       AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  FEMALE                        7                          1
  MALE                         10                          7
                            vv
clus                         N0 N1B N2C N3
  AMP PEAK 2(1Q44) MUTATED    9   2   2  2
  AMP PEAK 2(1Q44) WILD-TYPE  7   1   0  0
D2V5, multiclass
     clus
vv    AMP PEAK 2(1Q44) MUTATED AMP PEAK 2(1Q44) WILD-TYPE
  N0                         9                          7
  N1B                        2                          1
  N2C                        2                          0
  N3                         2                          0
D2V6, continuous
                            vv
clus                         STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 2(1Q44) MUTATED          0        1        5         1          3
  AMP PEAK 2(1Q44) WILD-TYPE        3        0        1         2          0
                            vv
clus                         STAGE IIIC STAGE IV
  AMP PEAK 2(1Q44) MUTATED            3        1
  AMP PEAK 2(1Q44) WILD-TYPE          1        0
D2V7, multiclass

Clustering(3) Variable = Amp Peak 3(7p22.3) mutation analysis
D3V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 3(7P22.3) MUTATED    4 10
  AMP PEAK 3(7P22.3) WILD-TYPE  5  6
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          14                           11 
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                          10                            6 
$`AMP PEAK 3(7P22.3) MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2GO 
       20.38        68.09        33.73         2.56        18.58       101.95 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZZ 
       96.23       136.44        26.73        20.91        27.68        27.02 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$`AMP PEAK 3(7P22.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC 
       48.76        29.82        14.70        25.87        24.43        43.23 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZP 
       14.30       204.62        41.59        26.37        74.73 

  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                         0.2                         14.3 
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                      136.44                       204.62 
  AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE 
                      26.875                       29.820 
[1] "0.2 - 136.4 (26.9)"  "14.3 - 204.6 (29.8)"
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 3(7P22.3) WILD-TYPE" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 3(7P22.3) WILD-TYPE"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "AMP PEAK 3(7P22.3) MUTATED" "AMP PEAK 3(7P22.3) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 3(7P22.3) MUTATED"   "AMP PEAK 3(7P22.3) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 3(7P22.3) MUTATED" 
[1] "hr=" "1.7"
D3V2, continuous
                              vv
clus                           DISTANT METASTASIS
  AMP PEAK 3(7P22.3) MUTATED                    4
  AMP PEAK 3(7P22.3) WILD-TYPE                  3
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 3(7P22.3) MUTATED                                                                                          4
  AMP PEAK 3(7P22.3) WILD-TYPE                                                                                        1
                              vv
clus                           REGIONAL LYMPH NODE
  AMP PEAK 3(7P22.3) MUTATED                     6
  AMP PEAK 3(7P22.3) WILD-TYPE                   7
D3V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 3(7P22.3) MUTATED
  DISTANT METASTASIS                                                                                                4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          4
  REGIONAL LYMPH NODE                                                                                               6
                                                                                          clus
vv                                                                                         AMP PEAK 3(7P22.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 7
D3V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(7P22.3) MUTATED      7    7
  AMP PEAK 3(7P22.3) WILD-TYPE    1   10
        clus
vv       AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  FEMALE                          7                            1
  MALE                            7                           10
                              vv
clus                           N0 N1B N2C N3
  AMP PEAK 3(7P22.3) MUTATED    8   0   2  2
  AMP PEAK 3(7P22.3) WILD-TYPE  8   3   0  0
D3V5, multiclass
     clus
vv    AMP PEAK 3(7P22.3) MUTATED AMP PEAK 3(7P22.3) WILD-TYPE
  N0                           8                            8
  N1B                          0                            3
  N2C                          2                            0
  N3                           2                            0
D3V6, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 3(7P22.3) MUTATED          1        0        4         1          2
  AMP PEAK 3(7P22.3) WILD-TYPE        2        1        2         2          1
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 3(7P22.3) MUTATED            2        1
  AMP PEAK 3(7P22.3) WILD-TYPE          2        0
D3V7, multiclass

Clustering(4) Variable = Amp Peak 4(7q36.1) mutation analysis
D4V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 4(7Q36.1) MUTATED    4 10
  AMP PEAK 4(7Q36.1) WILD-TYPE  5  6
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          14                           11 
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                          10                            6 
$`AMP PEAK 4(7Q36.1) MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       20.38        68.09        33.73        14.70         2.56        18.58 
TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1ZP TCGA-FS-A1ZZ 
      101.95        96.23       136.44        26.73        74.73        27.02 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$`AMP PEAK 4(7Q36.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
       48.76        29.82        25.87        24.43        43.23        14.30 
TCGA-EE-A2MI TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      204.62        41.59        26.37        20.91        27.68 

  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                         0.2                         14.3 
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                      136.44                       204.62 
  AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE 
                      26.875                       27.680 
[1] "0.2 - 136.4 (26.9)"  "14.3 - 204.6 (27.7)"
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 4(7Q36.1) MUTATED" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 4(7Q36.1) MUTATED" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "AMP PEAK 4(7Q36.1) MUTATED" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"AMP PEAK 4(7Q36.1) WILD-TYPE" "AMP PEAK 4(7Q36.1) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
"AMP PEAK 4(7Q36.1) WILD-TYPE"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
  "AMP PEAK 4(7Q36.1) MUTATED"   "AMP PEAK 4(7Q36.1) MUTATED" 
                  TCGA-GN-A266 
  "AMP PEAK 4(7Q36.1) MUTATED" 
[1] "hr=" "1.5"
D4V2, continuous
                              vv
clus                           DISTANT METASTASIS
  AMP PEAK 4(7Q36.1) MUTATED                    3
  AMP PEAK 4(7Q36.1) WILD-TYPE                  4
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 4(7Q36.1) MUTATED                                                                                          4
  AMP PEAK 4(7Q36.1) WILD-TYPE                                                                                        1
                              vv
clus                           REGIONAL LYMPH NODE
  AMP PEAK 4(7Q36.1) MUTATED                     7
  AMP PEAK 4(7Q36.1) WILD-TYPE                   6
D4V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 4(7Q36.1) MUTATED
  DISTANT METASTASIS                                                                                                3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          4
  REGIONAL LYMPH NODE                                                                                               7
                                                                                          clus
vv                                                                                         AMP PEAK 4(7Q36.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                  4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 6
D4V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(7Q36.1) MUTATED      6    8
  AMP PEAK 4(7Q36.1) WILD-TYPE    2    9
        clus
vv       AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  FEMALE                          6                            2
  MALE                            8                            9
                              vv
clus                           N0 N1B N2C N3
  AMP PEAK 4(7Q36.1) MUTATED    9   1   1  2
  AMP PEAK 4(7Q36.1) WILD-TYPE  7   2   1  0
D4V5, multiclass
     clus
vv    AMP PEAK 4(7Q36.1) MUTATED AMP PEAK 4(7Q36.1) WILD-TYPE
  N0                           9                            7
  N1B                          1                            2
  N2C                          1                            1
  N3                           2                            0
D4V6, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 4(7Q36.1) MUTATED          1        0        5         1          1
  AMP PEAK 4(7Q36.1) WILD-TYPE        2        1        1         2          2
                              vv
clus                           STAGE IIIC STAGE IV
  AMP PEAK 4(7Q36.1) MUTATED            3        1
  AMP PEAK 4(7Q36.1) WILD-TYPE          1        0
D4V7, multiclass

Clustering(5) Variable = Amp Peak 5(12p12.1) mutation analysis
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 5(12P12.1) MUTATED    1  2
  AMP PEAK 5(12P12.1) WILD-TYPE  8 14
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            3                            22 
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            2                            14 
$`AMP PEAK 5(12P12.1) MUTATED`
TCGA-EE-A29V TCGA-EE-A2MT TCGA-GN-A266 
       25.87        41.59        10.09 

$`AMP PEAK 5(12P12.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
        2.56        18.58        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
      204.62        96.23       136.44        26.73        26.37        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.68        74.73        27.02         0.20 

  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                        10.09                          0.20 
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                        41.59                        204.62 
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                        25.87                         27.35 
[1] "10.1 - 41.6 (25.9)" "0.2 - 204.6 (27.4)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-GN-A266 
  "AMP PEAK 5(12P12.1) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-GN-A266 
  "AMP PEAK 5(12P12.1) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 5(12P12.1) MUTATED" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-GN-A266 
  "AMP PEAK 5(12P12.1) MUTATED" 
[1] "hr=" "1.8"
D5V2, continuous
                               vv
clus                            DISTANT METASTASIS
  AMP PEAK 5(12P12.1) MUTATED                    1
  AMP PEAK 5(12P12.1) WILD-TYPE                  6
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 5(12P12.1) MUTATED                                                                                          1
  AMP PEAK 5(12P12.1) WILD-TYPE                                                                                        4
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK 5(12P12.1) MUTATED                     1
  AMP PEAK 5(12P12.1) WILD-TYPE                  12
D5V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 5(12P12.1) MUTATED
  DISTANT METASTASIS                                                                                                 1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                                1
                                                                                          clus
vv                                                                                         AMP PEAK 5(12P12.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                   6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             4
  REGIONAL LYMPH NODE                                                                                                 12
D5V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12P12.1) MUTATED      0    3
  AMP PEAK 5(12P12.1) WILD-TYPE    8   14
        clus
vv       AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE
  FEMALE                           0                             8
  MALE                             3                            14
                               vv
clus                            N0 N1B N2C N3
  AMP PEAK 5(12P12.1) MUTATED    1   1   0  0
  AMP PEAK 5(12P12.1) WILD-TYPE 15   2   2  2
D5V5, multiclass
[1] "Remove cluster labels:"      "AMP PEAK 5(12P12.1) MUTATED"
clus
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            2                            21 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2A2                    TCGA-EE-A2GC 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GO                    TCGA-EE-A2GR 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MI                    TCGA-EE-A2MJ 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MS                    TCGA-EE-A3AE 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1ZA 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZP                    TCGA-FS-A1ZZ 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FW-A3I3 
"AMP PEAK 5(12P12.1) WILD-TYPE" 
D5V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 5(12P12.1) MUTATED          0        1        0         0          0
  AMP PEAK 5(12P12.1) WILD-TYPE        3        0        6         3          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 5(12P12.1) MUTATED            1        0
  AMP PEAK 5(12P12.1) WILD-TYPE          3        1
D5V7, multiclass
[1] "Remove cluster labels:"      "AMP PEAK 5(12P12.1) MUTATED"
clus
  AMP PEAK 5(12P12.1) MUTATED AMP PEAK 5(12P12.1) WILD-TYPE 
                            2                            19 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A2A2 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-EE-A3AE                    TCGA-FS-A1ZA 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FS-A1ZP                    TCGA-FS-A1ZZ 
"AMP PEAK 5(12P12.1) WILD-TYPE" "AMP PEAK 5(12P12.1) WILD-TYPE" 
                   TCGA-FW-A3I3 
"AMP PEAK 5(12P12.1) WILD-TYPE" 

Clustering(6) Variable = Amp Peak 6(15q26.2) mutation analysis
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 6(15Q26.2) MUTATED    5  3
  AMP PEAK 6(15Q26.2) WILD-TYPE  4 13
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                            8                            17 
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                            3                            13 
$`AMP PEAK 6(15Q26.2) MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1Z3 
       48.76       101.95        96.23       136.44        26.73        20.91 
TCGA-FS-A1ZP TCGA-FW-A3I3 
       74.73         0.20 

$`AMP PEAK 6(15Q26.2) WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       20.38        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        24.43        43.23        14.30       204.62 
TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-GN-A266 
       41.59        26.37        27.68        27.02        10.09 

  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                         0.20                          2.56 
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                       136.44                        204.62 
  AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE 
                       61.745                        26.370 
[1] "0.2 - 136.4 (61.7)" "2.6 - 204.6 (26.4)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 6(15Q26.2) MUTATED" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "AMP PEAK 6(15Q26.2) MUTATED"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 6(15Q26.2) MUTATED" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "AMP PEAK 6(15Q26.2) MUTATED"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 6(15Q26.2) MUTATED" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"AMP PEAK 6(15Q26.2) WILD-TYPE" "AMP PEAK 6(15Q26.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "AMP PEAK 6(15Q26.2) MUTATED"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 6(15Q26.2) WILD-TYPE"   "AMP PEAK 6(15Q26.2) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 6(15Q26.2) WILD-TYPE" 
[1] "hr=" "3.8"
D6V2, continuous
                               vv
clus                            DISTANT METASTASIS
  AMP PEAK 6(15Q26.2) MUTATED                    3
  AMP PEAK 6(15Q26.2) WILD-TYPE                  4
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 6(15Q26.2) MUTATED                                                                                          1
  AMP PEAK 6(15Q26.2) WILD-TYPE                                                                                        4
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK 6(15Q26.2) MUTATED                     4
  AMP PEAK 6(15Q26.2) WILD-TYPE                   9
D6V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 6(15Q26.2) MUTATED
  DISTANT METASTASIS                                                                                                 3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
  REGIONAL LYMPH NODE                                                                                                4
                                                                                          clus
vv                                                                                         AMP PEAK 6(15Q26.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             4
  REGIONAL LYMPH NODE                                                                                                  9
D6V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(15Q26.2) MUTATED      4    4
  AMP PEAK 6(15Q26.2) WILD-TYPE    4   13
        clus
vv       AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  FEMALE                           4                             4
  MALE                             4                            13
                               vv
clus                            N0 N1B N2C N3
  AMP PEAK 6(15Q26.2) MUTATED    7   0   0  0
  AMP PEAK 6(15Q26.2) WILD-TYPE  9   3   2  2
D6V5, multiclass
     clus
vv    AMP PEAK 6(15Q26.2) MUTATED AMP PEAK 6(15Q26.2) WILD-TYPE
  N0                            7                             9
  N1B                           0                             3
  N2C                           0                             2
  N3                            0                             2
D6V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 6(15Q26.2) MUTATED          2        0        4         0          0
  AMP PEAK 6(15Q26.2) WILD-TYPE        1        1        2         3          3
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 6(15Q26.2) MUTATED            0        1
  AMP PEAK 6(15Q26.2) WILD-TYPE          4        0
D6V7, multiclass

Clustering(7) Variable = Amp Peak 7(17q25.3) mutation analysis
D7V1, survival
                               sevent
clus2                           0 1
  AMP PEAK 7(17Q25.3) MUTATED   7 8
  AMP PEAK 7(17Q25.3) WILD-TYPE 2 8
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                           15                            10 
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                            8                             8 
$`AMP PEAK 7(17Q25.3) MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       48.76        68.09        33.73        14.70         2.56        18.58 
TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT 
       25.87        43.23        14.30       204.62       136.44        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FW-A3I3 
       26.73        26.37         0.20 

$`AMP PEAK 7(17Q25.3) WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-FS-A1Z3 
       20.38        29.82        24.43       101.95        96.23        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       27.68        74.73        27.02        10.09 

  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                         0.20                         10.09 
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                       204.62                        101.95 
  AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE 
                        26.73                         27.35 
[1] "0.2 - 204.6 (26.7)"  "10.1 - 102.0 (27.4)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 7(17Q25.3) WILD-TYPE" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 7(17Q25.3) WILD-TYPE" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "AMP PEAK 7(17Q25.3) MUTATED"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "AMP PEAK 7(17Q25.3) MUTATED" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"AMP PEAK 7(17Q25.3) WILD-TYPE" "AMP PEAK 7(17Q25.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"AMP PEAK 7(17Q25.3) WILD-TYPE"   "AMP PEAK 7(17Q25.3) MUTATED" 
                   TCGA-GN-A266 
"AMP PEAK 7(17Q25.3) WILD-TYPE" 
[1] "hr=" "1.5"
D7V2, continuous
                               vv
clus                            DISTANT METASTASIS
  AMP PEAK 7(17Q25.3) MUTATED                    4
  AMP PEAK 7(17Q25.3) WILD-TYPE                  3
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 7(17Q25.3) MUTATED                                                                                          2
  AMP PEAK 7(17Q25.3) WILD-TYPE                                                                                        3
                               vv
clus                            REGIONAL LYMPH NODE
  AMP PEAK 7(17Q25.3) MUTATED                     9
  AMP PEAK 7(17Q25.3) WILD-TYPE                   4
D7V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 7(17Q25.3) MUTATED
  DISTANT METASTASIS                                                                                                 4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           2
  REGIONAL LYMPH NODE                                                                                                9
                                                                                          clus
vv                                                                                         AMP PEAK 7(17Q25.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             3
  REGIONAL LYMPH NODE                                                                                                  4
D7V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(17Q25.3) MUTATED      4   11
  AMP PEAK 7(17Q25.3) WILD-TYPE    4    6
        clus
vv       AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  FEMALE                           4                             4
  MALE                            11                             6
                               vv
clus                            N0 N1B N2C N3
  AMP PEAK 7(17Q25.3) MUTATED   11   2   1  1
  AMP PEAK 7(17Q25.3) WILD-TYPE  5   1   1  1
D7V5, multiclass
     clus
vv    AMP PEAK 7(17Q25.3) MUTATED AMP PEAK 7(17Q25.3) WILD-TYPE
  N0                           11                             5
  N1B                           2                             1
  N2C                           1                             1
  N3                            1                             1
D7V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  AMP PEAK 7(17Q25.3) MUTATED          2        1        3         2          1
  AMP PEAK 7(17Q25.3) WILD-TYPE        1        0        3         1          2
                               vv
clus                            STAGE IIIC STAGE IV
  AMP PEAK 7(17Q25.3) MUTATED            3        1
  AMP PEAK 7(17Q25.3) WILD-TYPE          1        0
D7V7, multiclass

Clustering(8) Variable = Del Peak  1(1p36.31) mutation analysis
D8V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.31) MUTATED    4  2
  DEL PEAK  1(1P36.31) WILD-TYPE  5 14
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             6                             19 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             2                             14 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-DA-A1I0 TCGA-EE-A182 TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MS TCGA-FW-A3I3 
       20.38        14.70       101.95        14.30       136.44         0.20 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N 
       48.76        68.09        29.82        33.73         2.56        18.58 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       25.87        24.43        43.23       204.62        96.23        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       26.73        26.37        20.91        27.68        74.73        27.02 
TCGA-GN-A266 
       10.09 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          0.20                           2.56 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                        136.44                         204.62 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         17.54                          27.68 
[1] "0.2 - 136.4 (17.5)" "2.6 - 204.6 (27.7)"
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  1(1P36.31) MUTATED" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
"DEL PEAK  1(1P36.31) WILD-TYPE" "DEL PEAK  1(1P36.31) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  1(1P36.31) WILD-TYPE"   "DEL PEAK  1(1P36.31) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK  1(1P36.31) WILD-TYPE" 
[1] "hr=" "1.9"
D8V2, continuous
                                vv
clus                             DISTANT METASTASIS
  DEL PEAK  1(1P36.31) MUTATED                    2
  DEL PEAK  1(1P36.31) WILD-TYPE                  5
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  1(1P36.31) MUTATED                                                                                          3
  DEL PEAK  1(1P36.31) WILD-TYPE                                                                                        2
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  1(1P36.31) MUTATED                     1
  DEL PEAK  1(1P36.31) WILD-TYPE                  12
D8V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P36.31) MUTATED
  DISTANT METASTASIS                                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 1
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P36.31) WILD-TYPE
  DISTANT METASTASIS                                                                                                    5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
  REGIONAL LYMPH NODE                                                                                                  12
D8V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      3    3
  DEL PEAK  1(1P36.31) WILD-TYPE    5   14
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                            3                              5
  MALE                              3                             14
                                vv
clus                             N0 N1B N2C N3
  DEL PEAK  1(1P36.31) MUTATED    4   1   0  1
  DEL PEAK  1(1P36.31) WILD-TYPE 12   2   2  1
D8V5, multiclass
     clus
vv    DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                             4                             12
  N1B                            1                              2
  N2C                            0                              2
  N3                             1                              1
D8V6, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK  1(1P36.31) MUTATED          0        0        3         0
  DEL PEAK  1(1P36.31) WILD-TYPE        3        1        3         3
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  1(1P36.31) MUTATED            0          2        1
  DEL PEAK  1(1P36.31) WILD-TYPE          3          2        0
D8V7, multiclass

Clustering(9) Variable = Del Peak  2(1p13.2) mutation analysis
D9V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.2) MUTATED    6  3
  DEL PEAK  2(1P13.2) WILD-TYPE  3 13
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            9                            16 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                            3                            13 
$`DEL PEAK  2(1P13.2) MUTATED`
TCGA-DA-A1I0 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MS 
       20.38        43.23       101.95        14.30       204.62       136.44 
TCGA-EE-A3AE TCGA-FS-A1ZA TCGA-FW-A3I3 
       26.73        27.68         0.20 

$`DEL PEAK  2(1P13.2) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       48.76        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F 
       18.58        25.87        24.43        96.23        41.59        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       20.91        74.73        27.02        10.09 

  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                         0.20                          2.56 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       204.62                         96.23 
  DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE 
                       27.680                        26.695 
[1] "0.2 - 204.6 (27.7)" "2.6 - 96.2 (26.7)" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  2(1P13.2) MUTATED"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  2(1P13.2) WILD-TYPE" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  2(1P13.2) MUTATED" "DEL PEAK  2(1P13.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  2(1P13.2) WILD-TYPE"   "DEL PEAK  2(1P13.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  2(1P13.2) WILD-TYPE" 
[1] "hr=" "5.1"
D9V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK  2(1P13.2) MUTATED                    2
  DEL PEAK  2(1P13.2) WILD-TYPE                  5
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  2(1P13.2) MUTATED                                                                                          3
  DEL PEAK  2(1P13.2) WILD-TYPE                                                                                        2
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  2(1P13.2) MUTATED                     4
  DEL PEAK  2(1P13.2) WILD-TYPE                   9
D9V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  2(1P13.2) MUTATED
  DISTANT METASTASIS                                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           3
  REGIONAL LYMPH NODE                                                                                                4
                                                                                          clus
vv                                                                                         DEL PEAK  2(1P13.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
  REGIONAL LYMPH NODE                                                                                                  9
D9V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.2) MUTATED      4    5
  DEL PEAK  2(1P13.2) WILD-TYPE    4   12
        clus
vv       DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  FEMALE                           4                             4
  MALE                             5                            12
                               vv
clus                            N0 N1B N2C N3
  DEL PEAK  2(1P13.2) MUTATED    7   0   1  1
  DEL PEAK  2(1P13.2) WILD-TYPE  9   3   1  1
D9V5, multiclass
     clus
vv    DEL PEAK  2(1P13.2) MUTATED DEL PEAK  2(1P13.2) WILD-TYPE
  N0                            7                             9
  N1B                           0                             3
  N2C                           1                             1
  N3                            1                             1
D9V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK  2(1P13.2) MUTATED          1        0        3         2          1
  DEL PEAK  2(1P13.2) WILD-TYPE        2        1        3         1          2
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  2(1P13.2) MUTATED            1        1
  DEL PEAK  2(1P13.2) WILD-TYPE          3        0
D9V7, multiclass

Clustering(10) Variable = Del Peak  3(2q37.3) mutation analysis
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(2Q37.3) MUTATED    4  4
  DEL PEAK  3(2Q37.3) WILD-TYPE  5 12
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            8                            17 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                            4                            12 
$`DEL PEAK  3(2Q37.3) MUTATED`
TCGA-DA-A1I0 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-FS-A1ZZ 
       20.38        43.23        14.30        96.23       136.44        27.02 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

$`DEL PEAK  3(2Q37.3) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       48.76        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MT 
       18.58        25.87        24.43       101.95       204.62        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP 
       26.73        26.37        20.91        27.68        74.73 

  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                         0.20                          2.56 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                       136.44                        204.62 
  DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE 
                        23.70                         27.68 
[1] "0.2 - 136.4 (23.7)" "2.6 - 204.6 (27.7)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
"DEL PEAK  3(2Q37.3) WILD-TYPE"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  3(2Q37.3) MUTATED" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
"DEL PEAK  3(2Q37.3) WILD-TYPE" "DEL PEAK  3(2Q37.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  3(2Q37.3) MUTATED"   "DEL PEAK  3(2Q37.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  3(2Q37.3) MUTATED" 
[1] "hr=" "1.2"
D10V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK  3(2Q37.3) MUTATED                    2
  DEL PEAK  3(2Q37.3) WILD-TYPE                  5
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  3(2Q37.3) MUTATED                                                                                          3
  DEL PEAK  3(2Q37.3) WILD-TYPE                                                                                        2
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  3(2Q37.3) MUTATED                     3
  DEL PEAK  3(2Q37.3) WILD-TYPE                  10
D10V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  3(2Q37.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           3
  REGIONAL LYMPH NODE                                                                                                3
                                                                                          clus
vv                                                                                         DEL PEAK  3(2Q37.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
  REGIONAL LYMPH NODE                                                                                                 10
D10V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q37.3) MUTATED      2    6
  DEL PEAK  3(2Q37.3) WILD-TYPE    6   11
        clus
vv       DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  FEMALE                           2                             6
  MALE                             6                            11
                               vv
clus                            N0 N1B N2C N3
  DEL PEAK  3(2Q37.3) MUTATED    6   0   0  1
  DEL PEAK  3(2Q37.3) WILD-TYPE 10   3   2  1
D10V5, multiclass
     clus
vv    DEL PEAK  3(2Q37.3) MUTATED DEL PEAK  3(2Q37.3) WILD-TYPE
  N0                            6                            10
  N1B                           0                             3
  N2C                           0                             2
  N3                            1                             1
D10V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK  3(2Q37.3) MUTATED          0        0        3         2          0
  DEL PEAK  3(2Q37.3) WILD-TYPE        3        1        3         1          3
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  3(2Q37.3) MUTATED            1        1
  DEL PEAK  3(2Q37.3) WILD-TYPE          3        0
D10V7, multiclass

Clustering(11) Variable = Del Peak  4(3q23) mutation analysis
D11V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  4(3Q23) MUTATED    2  1
  DEL PEAK  4(3Q23) WILD-TYPE  7 15
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          3                          22 
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          1                          15 
$`DEL PEAK  4(3Q23) MUTATED`
TCGA-EE-A2GC TCGA-ER-A19F TCGA-FW-A3I3 
       43.23        26.37         0.20 

$`DEL PEAK  4(3Q23) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR 
        2.56        18.58        25.87        24.43       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-FS-A1Z3 
      204.62        96.23       136.44        41.59        26.73        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       27.68        74.73        27.02        10.09 

  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                       0.20                        2.56 
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                      43.23                      204.62 
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                      26.37                       27.35 
[1] "0.2 - 43.2 (26.4)"  "2.6 - 204.6 (27.4)"
                 TCGA-D3-A2JF                  TCGA-DA-A1I0 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-DA-A1IC                  TCGA-EE-A17X 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A181                  TCGA-EE-A182 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29L                  TCGA-EE-A29N 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29V                  TCGA-EE-A2A2 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GC                  TCGA-EE-A2GO 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GR                  TCGA-EE-A2MI 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MJ                  TCGA-EE-A2MS 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MT                  TCGA-EE-A3AE 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-FS-A1Z3 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZA                  TCGA-FS-A1ZP 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZZ                  TCGA-FW-A3I3 
"DEL PEAK  4(3Q23) WILD-TYPE"   "DEL PEAK  4(3Q23) MUTATED" 
                 TCGA-GN-A266 
"DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-D3-A2JF                  TCGA-DA-A1I0 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-DA-A1IC                  TCGA-EE-A17X 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A181                  TCGA-EE-A182 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29L                  TCGA-EE-A29N 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29V                  TCGA-EE-A2A2 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GC                  TCGA-EE-A2GO 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GR                  TCGA-EE-A2MI 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MJ                  TCGA-EE-A2MS 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MT                  TCGA-EE-A3AE 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-FS-A1Z3 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZA                  TCGA-FS-A1ZP 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZZ                  TCGA-FW-A3I3 
"DEL PEAK  4(3Q23) WILD-TYPE"   "DEL PEAK  4(3Q23) MUTATED" 
                 TCGA-GN-A266 
"DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-D3-A2JF                  TCGA-DA-A1I0 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-DA-A1IC                  TCGA-EE-A17X 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A181                  TCGA-EE-A182 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29L                  TCGA-EE-A29N 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29V                  TCGA-EE-A2A2 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GC                  TCGA-EE-A2GO 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GR                  TCGA-EE-A2MI 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MJ                  TCGA-EE-A2MS 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MT                  TCGA-EE-A3AE 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-ER-A19F                  TCGA-FS-A1Z3 
  "DEL PEAK  4(3Q23) MUTATED" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZA                  TCGA-FS-A1ZP 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZZ                  TCGA-FW-A3I3 
"DEL PEAK  4(3Q23) WILD-TYPE"   "DEL PEAK  4(3Q23) MUTATED" 
                 TCGA-GN-A266 
"DEL PEAK  4(3Q23) WILD-TYPE" 
[1] "hr=" "1.2"
D11V2, continuous
                             vv
clus                          DISTANT METASTASIS
  DEL PEAK  4(3Q23) MUTATED                    1
  DEL PEAK  4(3Q23) WILD-TYPE                  6
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  4(3Q23) MUTATED                                                                                          0
  DEL PEAK  4(3Q23) WILD-TYPE                                                                                        5
                             vv
clus                          REGIONAL LYMPH NODE
  DEL PEAK  4(3Q23) MUTATED                     2
  DEL PEAK  4(3Q23) WILD-TYPE                  11
D11V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  4(3Q23) MUTATED
  DISTANT METASTASIS                                                                                               1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         0
  REGIONAL LYMPH NODE                                                                                              2
                                                                                          clus
vv                                                                                         DEL PEAK  4(3Q23) WILD-TYPE
  DISTANT METASTASIS                                                                                                 6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           5
  REGIONAL LYMPH NODE                                                                                               11
D11V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(3Q23) MUTATED      1    2
  DEL PEAK  4(3Q23) WILD-TYPE    7   15
        clus
vv       DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  FEMALE                         1                           7
  MALE                           2                          15
                             vv
clus                          N0 N1B N2C N3
  DEL PEAK  4(3Q23) MUTATED    3   0   0  0
  DEL PEAK  4(3Q23) WILD-TYPE 13   3   2  2
D11V5, multiclass
     clus
vv    DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE
  N0                          3                          13
  N1B                         0                           3
  N2C                         0                           2
  N3                          0                           2
D11V6, continuous
                             vv
clus                          STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK  4(3Q23) MUTATED          0        0        0         1          0
  DEL PEAK  4(3Q23) WILD-TYPE        3        1        6         2          3
                             vv
clus                          STAGE IIIC STAGE IV
  DEL PEAK  4(3Q23) MUTATED            0        1
  DEL PEAK  4(3Q23) WILD-TYPE          4        0
D11V7, multiclass
[1] "Remove cluster labels:"    "DEL PEAK  4(3Q23) MUTATED"
clus
  DEL PEAK  4(3Q23) MUTATED DEL PEAK  4(3Q23) WILD-TYPE 
                          2                          19 
                 TCGA-D3-A2JF                  TCGA-DA-A1I0 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-DA-A1IC                  TCGA-EE-A17X 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A181                  TCGA-EE-A182 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A29L                  TCGA-EE-A29V 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2A2                  TCGA-EE-A2GO 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2GR                  TCGA-EE-A2MI 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MJ                  TCGA-EE-A2MS 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-EE-A2MT                  TCGA-EE-A3AE 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZA                  TCGA-FS-A1ZP 
"DEL PEAK  4(3Q23) WILD-TYPE" "DEL PEAK  4(3Q23) WILD-TYPE" 
                 TCGA-FS-A1ZZ 
"DEL PEAK  4(3Q23) WILD-TYPE" 

Clustering(12) Variable = Del Peak  5(6q23.2) mutation analysis
D12V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  5(6Q23.2) MUTATED   6 8
  DEL PEAK  5(6Q23.2) WILD-TYPE 3 8
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                           14                            11 
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                            8                             8 
$`DEL PEAK  5(6Q23.2) MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       48.76        68.09        33.73        14.70         2.56        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZA 
       24.43       101.95       136.44        41.59        26.37        27.68 
TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.02         0.20 

$`DEL PEAK  5(6Q23.2) WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI 
       20.38        29.82        18.58        43.23        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A3AE TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-GN-A266 
       96.23        26.73        20.91        74.73        10.09 

  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                         0.20                         10.09 
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                       136.44                        204.62 
  DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE 
                        27.35                         26.73 
[1] "0.2 - 136.4 (27.4)"  "10.1 - 204.6 (26.7)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"DEL PEAK  5(6Q23.2) WILD-TYPE" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"DEL PEAK  5(6Q23.2) WILD-TYPE" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
"DEL PEAK  5(6Q23.2) WILD-TYPE" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  5(6Q23.2) WILD-TYPE"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  5(6Q23.2) MUTATED" "DEL PEAK  5(6Q23.2) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
  "DEL PEAK  5(6Q23.2) MUTATED"   "DEL PEAK  5(6Q23.2) MUTATED" 
                   TCGA-GN-A266 
"DEL PEAK  5(6Q23.2) WILD-TYPE" 
[1] "hr=" "1.1"
D12V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK  5(6Q23.2) MUTATED                    6
  DEL PEAK  5(6Q23.2) WILD-TYPE                  1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  5(6Q23.2) MUTATED                                                                                          2
  DEL PEAK  5(6Q23.2) WILD-TYPE                                                                                        3
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  5(6Q23.2) MUTATED                     6
  DEL PEAK  5(6Q23.2) WILD-TYPE                   7
D12V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  5(6Q23.2) MUTATED
  DISTANT METASTASIS                                                                                                 6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           2
  REGIONAL LYMPH NODE                                                                                                6
                                                                                          clus
vv                                                                                         DEL PEAK  5(6Q23.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             3
  REGIONAL LYMPH NODE                                                                                                  7
D12V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q23.2) MUTATED      6    8
  DEL PEAK  5(6Q23.2) WILD-TYPE    2    9
        clus
vv       DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  FEMALE                           6                             2
  MALE                             8                             9
                               vv
clus                            N0 N1B N2C N3
  DEL PEAK  5(6Q23.2) MUTATED    8   3   2  1
  DEL PEAK  5(6Q23.2) WILD-TYPE  8   0   0  1
D12V5, multiclass
     clus
vv    DEL PEAK  5(6Q23.2) MUTATED DEL PEAK  5(6Q23.2) WILD-TYPE
  N0                            8                             8
  N1B                           3                             0
  N2C                           2                             0
  N3                            1                             1
D12V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK  5(6Q23.2) MUTATED          1        1        3         1          3
  DEL PEAK  5(6Q23.2) WILD-TYPE        2        0        3         2          0
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  5(6Q23.2) MUTATED            3        1
  DEL PEAK  5(6Q23.2) WILD-TYPE          1        0
D12V7, multiclass

Clustering(13) Variable = Del Peak  6(9p21.3) mutation analysis
D13V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(9P21.3) MUTATED    7 12
  DEL PEAK  6(9P21.3) WILD-TYPE  2  4
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           19                             6 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                           12                             4 
$`DEL PEAK  6(9P21.3) MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       48.76        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        43.23       101.95        14.30       204.62 
TCGA-EE-A2MS TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FW-A3I3 
      136.44        26.73        26.37        20.91        27.68         0.20 
TCGA-GN-A266 
       10.09 

$`DEL PEAK  6(9P21.3) WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A2A2 TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       20.38        24.43        96.23        41.59        74.73        27.02 

  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                         0.20                         20.38 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                       204.62                         96.23 
  DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE 
                       26.730                        34.305 
[1] "0.2 - 204.6 (26.7)" "20.4 - 96.2 (34.3)"
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-D3-A2JF                    TCGA-DA-A1I0 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-DA-A1IC                    TCGA-EE-A17X 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A181                    TCGA-EE-A182 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29L                    TCGA-EE-A29N 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A29V                    TCGA-EE-A2A2 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-EE-A2GC                    TCGA-EE-A2GO 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2GR                    TCGA-EE-A2MI 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MJ                    TCGA-EE-A2MS 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-EE-A2MT                    TCGA-EE-A3AE 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-ER-A19F                    TCGA-FS-A1Z3 
  "DEL PEAK  6(9P21.3) MUTATED"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-FS-A1ZA                    TCGA-FS-A1ZP 
  "DEL PEAK  6(9P21.3) MUTATED" "DEL PEAK  6(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZZ                    TCGA-FW-A3I3 
"DEL PEAK  6(9P21.3) WILD-TYPE"   "DEL PEAK  6(9P21.3) MUTATED" 
                   TCGA-GN-A266 
  "DEL PEAK  6(9P21.3) MUTATED" 
[1] "hr=" "1.1"
D13V2, continuous
                               vv
clus                            DISTANT METASTASIS
  DEL PEAK  6(9P21.3) MUTATED                    6
  DEL PEAK  6(9P21.3) WILD-TYPE                  1
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  6(9P21.3) MUTATED                                                                                          4
  DEL PEAK  6(9P21.3) WILD-TYPE                                                                                        1
                               vv
clus                            REGIONAL LYMPH NODE
  DEL PEAK  6(9P21.3) MUTATED                     9
  DEL PEAK  6(9P21.3) WILD-TYPE                   4
D13V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  6(9P21.3) MUTATED
  DISTANT METASTASIS                                                                                                 6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           4
  REGIONAL LYMPH NODE                                                                                                9
                                                                                          clus
vv                                                                                         DEL PEAK  6(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
  REGIONAL LYMPH NODE                                                                                                  4
D13V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(9P21.3) MUTATED      7   12
  DEL PEAK  6(9P21.3) WILD-TYPE    1    5
        clus
vv       DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  FEMALE                           7                             1
  MALE                            12                             5
                               vv
clus                            N0 N1B N2C N3
  DEL PEAK  6(9P21.3) MUTATED   12   2   2  1
  DEL PEAK  6(9P21.3) WILD-TYPE  4   1   0  1
D13V5, multiclass
     clus
vv    DEL PEAK  6(9P21.3) MUTATED DEL PEAK  6(9P21.3) WILD-TYPE
  N0                           12                             4
  N1B                           2                             1
  N2C                           2                             0
  N3                            1                             1
D13V6, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK  6(9P21.3) MUTATED          3        0        4         2          2
  DEL PEAK  6(9P21.3) WILD-TYPE        0        1        2         1          1
                               vv
clus                            STAGE IIIC STAGE IV
  DEL PEAK  6(9P21.3) MUTATED            3        1
  DEL PEAK  6(9P21.3) WILD-TYPE          1        0
D13V7, multiclass

Clustering(14) Variable = Del Peak  7(10p15.1) mutation analysis
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  7(10P15.1) MUTATED    5  6
  DEL PEAK  7(10P15.1) WILD-TYPE  4 10
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                            11                             14 
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                             6                             10 
$`DEL PEAK  7(10P15.1) MUTATED`
TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI 
       33.73         2.56        24.43       101.95        14.30       204.62 
TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-GN-A266 
      136.44        26.73        20.91        27.68        10.09 

$`DEL PEAK  7(10P15.1) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N 
       48.76        20.38        68.09        29.82        14.70        18.58 
TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZP 
       25.87        43.23        96.23        41.59        26.37        74.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.02         0.20 

  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                          2.56                           0.20 
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                        204.62                          96.23 
  DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE 
                         26.73                          28.42 
[1] "2.6 - 204.6 (26.7)" "0.2 - 96.2 (28.4)" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  7(10P15.1) MUTATED"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-GN-A266 
  "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  7(10P15.1) MUTATED"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-GN-A266 
  "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  7(10P15.1) MUTATED"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK  7(10P15.1) WILD-TYPE"   "DEL PEAK  7(10P15.1) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  7(10P15.1) MUTATED" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK  7(10P15.1) WILD-TYPE" "DEL PEAK  7(10P15.1) WILD-TYPE" 
                    TCGA-GN-A266 
  "DEL PEAK  7(10P15.1) MUTATED" 
[1] "hr=" "1.7"
D14V2, continuous
                                vv
clus                             DISTANT METASTASIS
  DEL PEAK  7(10P15.1) MUTATED                    2
  DEL PEAK  7(10P15.1) WILD-TYPE                  5
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  7(10P15.1) MUTATED                                                                                          3
  DEL PEAK  7(10P15.1) WILD-TYPE                                                                                        2
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  7(10P15.1) MUTATED                     6
  DEL PEAK  7(10P15.1) WILD-TYPE                   7
D14V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  7(10P15.1) MUTATED
  DISTANT METASTASIS                                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 6
                                                                                          clus
vv                                                                                         DEL PEAK  7(10P15.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
  REGIONAL LYMPH NODE                                                                                                   7
D14V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(10P15.1) MUTATED      5    6
  DEL PEAK  7(10P15.1) WILD-TYPE    3   11
        clus
vv       DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  FEMALE                            5                              3
  MALE                              6                             11
                                vv
clus                             N0 N1B N2C N3
  DEL PEAK  7(10P15.1) MUTATED    6   1   1  1
  DEL PEAK  7(10P15.1) WILD-TYPE 10   2   1  1
D14V5, multiclass
     clus
vv    DEL PEAK  7(10P15.1) MUTATED DEL PEAK  7(10P15.1) WILD-TYPE
  N0                             6                             10
  N1B                            1                              2
  N2C                            1                              1
  N3                             1                              1
D14V6, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK  7(10P15.1) MUTATED          1        0        4         1
  DEL PEAK  7(10P15.1) WILD-TYPE        2        1        2         2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  7(10P15.1) MUTATED            2          1        0
  DEL PEAK  7(10P15.1) WILD-TYPE          1          3        1
D14V7, multiclass

Clustering(15) Variable = Del Peak  8(10q24.33) mutation analysis
D15V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK  8(10Q24.33) MUTATED    6  6
  DEL PEAK  8(10Q24.33) WILD-TYPE  3 10
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                             12                              13 
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                              6                              10 
$`DEL PEAK  8(10Q24.33) MUTATED`
TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       33.73         2.56        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A3AE TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FW-A3I3 TCGA-GN-A266 
      204.62        26.73        20.91        27.68         0.20        10.09 

$`DEL PEAK  8(10Q24.33) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N 
       48.76        20.38        68.09        29.82        14.70        18.58 
TCGA-EE-A29V TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZP 
       25.87        96.23       136.44        41.59        26.37        74.73 
TCGA-FS-A1ZZ 
       27.02 

  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                            0.2                            14.7 
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                         204.62                          136.44 
  DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE 
                          25.58                           29.82 
[1] "0.2 - 204.6 (25.6)"  "14.7 - 136.4 (29.8)"
                     TCGA-D3-A2JF                      TCGA-DA-A1I0 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-DA-A1IC                      TCGA-EE-A17X 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A181                      TCGA-EE-A182 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29L                      TCGA-EE-A29N 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29V                      TCGA-EE-A2A2 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GC                      TCGA-EE-A2GO 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GR                      TCGA-EE-A2MI 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2MJ                      TCGA-EE-A2MS 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A2MT                      TCGA-EE-A3AE 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-ER-A19F                      TCGA-FS-A1Z3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-FS-A1ZA                      TCGA-FS-A1ZP 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-FS-A1ZZ                      TCGA-FW-A3I3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-GN-A266 
  "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-D3-A2JF                      TCGA-DA-A1I0 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-DA-A1IC                      TCGA-EE-A17X 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A181                      TCGA-EE-A182 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29L                      TCGA-EE-A29N 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29V                      TCGA-EE-A2A2 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GC                      TCGA-EE-A2GO 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GR                      TCGA-EE-A2MI 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2MJ                      TCGA-EE-A2MS 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A2MT                      TCGA-EE-A3AE 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-ER-A19F                      TCGA-FS-A1Z3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-FS-A1ZA                      TCGA-FS-A1ZP 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-FS-A1ZZ                      TCGA-FW-A3I3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-GN-A266 
  "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-D3-A2JF                      TCGA-DA-A1I0 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-DA-A1IC                      TCGA-EE-A17X 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A181                      TCGA-EE-A182 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29L                      TCGA-EE-A29N 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A29V                      TCGA-EE-A2A2 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GC                      TCGA-EE-A2GO 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2GR                      TCGA-EE-A2MI 
  "DEL PEAK  8(10Q24.33) MUTATED"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-EE-A2MJ                      TCGA-EE-A2MS 
"DEL PEAK  8(10Q24.33) WILD-TYPE" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-EE-A2MT                      TCGA-EE-A3AE 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-ER-A19F                      TCGA-FS-A1Z3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-FS-A1ZA                      TCGA-FS-A1ZP 
  "DEL PEAK  8(10Q24.33) MUTATED" "DEL PEAK  8(10Q24.33) WILD-TYPE" 
                     TCGA-FS-A1ZZ                      TCGA-FW-A3I3 
"DEL PEAK  8(10Q24.33) WILD-TYPE"   "DEL PEAK  8(10Q24.33) MUTATED" 
                     TCGA-GN-A266 
  "DEL PEAK  8(10Q24.33) MUTATED" 
[1] "hr=" "1.4"
D15V2, continuous
                                 vv
clus                              DISTANT METASTASIS
  DEL PEAK  8(10Q24.33) MUTATED                    3
  DEL PEAK  8(10Q24.33) WILD-TYPE                  4
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  8(10Q24.33) MUTATED                                                                                          3
  DEL PEAK  8(10Q24.33) WILD-TYPE                                                                                        2
                                 vv
clus                              REGIONAL LYMPH NODE
  DEL PEAK  8(10Q24.33) MUTATED                     6
  DEL PEAK  8(10Q24.33) WILD-TYPE                   7
D15V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  8(10Q24.33) MUTATED
  DISTANT METASTASIS                                                                                                   3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             3
  REGIONAL LYMPH NODE                                                                                                  6
                                                                                          clus
vv                                                                                         DEL PEAK  8(10Q24.33) WILD-TYPE
  DISTANT METASTASIS                                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               2
  REGIONAL LYMPH NODE                                                                                                    7
D15V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  8(10Q24.33) MUTATED      6    6
  DEL PEAK  8(10Q24.33) WILD-TYPE    2   11
        clus
vv       DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  FEMALE                             6                               2
  MALE                               6                              11
                                 vv
clus                              N0 N1B N2C N3
  DEL PEAK  8(10Q24.33) MUTATED    7   1   1  1
  DEL PEAK  8(10Q24.33) WILD-TYPE  9   2   1  1
D15V5, multiclass
     clus
vv    DEL PEAK  8(10Q24.33) MUTATED DEL PEAK  8(10Q24.33) WILD-TYPE
  N0                              7                               9
  N1B                             1                               2
  N2C                             1                               1
  N3                              1                               1
D15V6, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK  8(10Q24.33) MUTATED          1        0        3         2
  DEL PEAK  8(10Q24.33) WILD-TYPE        2        1        3         1
                                 vv
clus                              STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  8(10Q24.33) MUTATED            2          1        1
  DEL PEAK  8(10Q24.33) WILD-TYPE          1          3        0
D15V7, multiclass

Clustering(16) Variable = Del Peak  9(11q24.3) mutation analysis
D16V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  9(11Q24.3) MUTATED    8 11
  DEL PEAK  9(11Q24.3) WILD-TYPE  1  5
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            19                              6 
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                            11                              5 
$`DEL PEAK  9(11Q24.3) MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 
       48.76        14.70         2.56        18.58        25.87        24.43 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT 
       43.23        14.30       204.62        96.23       136.44        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-FW-A3I3 
       26.73        26.37        20.91        27.68        27.02         0.20 
TCGA-GN-A266 
       10.09 

$`DEL PEAK  9(11Q24.3) WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A2GO TCGA-FS-A1ZP 
       20.38        68.09        29.82        33.73       101.95        74.73 

  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                          0.20                          20.38 
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                        204.62                         101.95 
  DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE 
                         26.37                          50.91 
[1] "0.2 - 204.6 (26.4)"  "20.4 - 102.0 (50.9)"
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  9(11Q24.3) WILD-TYPE" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  9(11Q24.3) WILD-TYPE"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-GN-A266 
  "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  9(11Q24.3) WILD-TYPE" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  9(11Q24.3) WILD-TYPE"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-GN-A266 
  "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK  9(11Q24.3) WILD-TYPE" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
"DEL PEAK  9(11Q24.3) WILD-TYPE"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK  9(11Q24.3) MUTATED" "DEL PEAK  9(11Q24.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
  "DEL PEAK  9(11Q24.3) MUTATED"   "DEL PEAK  9(11Q24.3) MUTATED" 
                    TCGA-GN-A266 
  "DEL PEAK  9(11Q24.3) MUTATED" 
[1] "hr=" "1"  
D16V2, continuous
                                vv
clus                             DISTANT METASTASIS
  DEL PEAK  9(11Q24.3) MUTATED                    7
  DEL PEAK  9(11Q24.3) WILD-TYPE                  0
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  9(11Q24.3) MUTATED                                                                                          2
  DEL PEAK  9(11Q24.3) WILD-TYPE                                                                                        3
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK  9(11Q24.3) MUTATED                    10
  DEL PEAK  9(11Q24.3) WILD-TYPE                   3
D16V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  9(11Q24.3) MUTATED
  DISTANT METASTASIS                                                                                                  7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            2
  REGIONAL LYMPH NODE                                                                                                10
                                                                                          clus
vv                                                                                         DEL PEAK  9(11Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              3
  REGIONAL LYMPH NODE                                                                                                   3
D16V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(11Q24.3) MUTATED      6   13
  DEL PEAK  9(11Q24.3) WILD-TYPE    2    4
        clus
vv       DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  FEMALE                            6                              2
  MALE                             13                              4
                                vv
clus                             N0 N1B N2C N3
  DEL PEAK  9(11Q24.3) MUTATED   12   3   1  1
  DEL PEAK  9(11Q24.3) WILD-TYPE  4   0   1  1
D16V5, multiclass
     clus
vv    DEL PEAK  9(11Q24.3) MUTATED DEL PEAK  9(11Q24.3) WILD-TYPE
  N0                            12                              4
  N1B                            3                              0
  N2C                            1                              1
  N3                             1                              1
D16V6, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK  9(11Q24.3) MUTATED          2        1        3         3
  DEL PEAK  9(11Q24.3) WILD-TYPE        1        0        3         0
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  9(11Q24.3) MUTATED            2          3        1
  DEL PEAK  9(11Q24.3) WILD-TYPE          1          1        0
D16V7, multiclass

Clustering(17) Variable = Del Peak 10(13q34) mutation analysis
D17V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 10(13Q34) MUTATED    2  5
  DEL PEAK 10(13Q34) WILD-TYPE  7 11
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           7                           18 
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                           5                           11 
$`DEL PEAK 10(13Q34) MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1ZA 
       68.09        33.73        18.58       136.44        26.73        27.68 
TCGA-GN-A266 
       10.09 

$`DEL PEAK 10(13Q34) WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       48.76        20.38        29.82        14.70         2.56        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       24.43        43.23       101.95        14.30       204.62        96.23 
TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       41.59        26.37        20.91        74.73        27.02         0.20 

  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                       10.09                         0.20 
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                      136.44                       204.62 
  DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE 
                      27.680                       26.695 
[1] "10.1 - 136.4 (27.7)" "0.2 - 204.6 (26.7)" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-GN-A266 
  "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-GN-A266 
  "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-D3-A2JF                   TCGA-DA-A1I0 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-DA-A1IC                   TCGA-EE-A17X 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A181                   TCGA-EE-A182 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A29L                   TCGA-EE-A29N 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A29V                   TCGA-EE-A2A2 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GC                   TCGA-EE-A2GO 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2GR                   TCGA-EE-A2MI 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-EE-A2MJ                   TCGA-EE-A2MS 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-EE-A2MT                   TCGA-EE-A3AE 
"DEL PEAK 10(13Q34) WILD-TYPE"   "DEL PEAK 10(13Q34) MUTATED" 
                  TCGA-ER-A19F                   TCGA-FS-A1Z3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZA                   TCGA-FS-A1ZP 
  "DEL PEAK 10(13Q34) MUTATED" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-FS-A1ZZ                   TCGA-FW-A3I3 
"DEL PEAK 10(13Q34) WILD-TYPE" "DEL PEAK 10(13Q34) WILD-TYPE" 
                  TCGA-GN-A266 
  "DEL PEAK 10(13Q34) MUTATED" 
[1] "hr=" "1.2"
D17V2, continuous
                              vv
clus                           DISTANT METASTASIS
  DEL PEAK 10(13Q34) MUTATED                    1
  DEL PEAK 10(13Q34) WILD-TYPE                  6
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 10(13Q34) MUTATED                                                                                          2
  DEL PEAK 10(13Q34) WILD-TYPE                                                                                        3
                              vv
clus                           REGIONAL LYMPH NODE
  DEL PEAK 10(13Q34) MUTATED                     4
  DEL PEAK 10(13Q34) WILD-TYPE                   9
D17V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 10(13Q34) MUTATED
  DISTANT METASTASIS                                                                                                1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          2
  REGIONAL LYMPH NODE                                                                                               4
                                                                                          clus
vv                                                                                         DEL PEAK 10(13Q34) WILD-TYPE
  DISTANT METASTASIS                                                                                                  6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            3
  REGIONAL LYMPH NODE                                                                                                 9
D17V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(13Q34) MUTATED      3    4
  DEL PEAK 10(13Q34) WILD-TYPE    5   13
        clus
vv       DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  FEMALE                          3                            5
  MALE                            4                           13
                              vv
clus                           N0 N1B N2C N3
  DEL PEAK 10(13Q34) MUTATED    4   0   2  0
  DEL PEAK 10(13Q34) WILD-TYPE 12   3   0  2
D17V5, multiclass
     clus
vv    DEL PEAK 10(13Q34) MUTATED DEL PEAK 10(13Q34) WILD-TYPE
  N0                           4                           12
  N1B                          0                            3
  N2C                          2                            0
  N3                           0                            2
D17V6, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB
  DEL PEAK 10(13Q34) MUTATED          1        0        2         0          2
  DEL PEAK 10(13Q34) WILD-TYPE        2        1        4         3          1
                              vv
clus                           STAGE IIIC STAGE IV
  DEL PEAK 10(13Q34) MUTATED            0        0
  DEL PEAK 10(13Q34) WILD-TYPE          4        1
D17V7, multiclass

Clustering(18) Variable = Del Peak 11(14q23.3) mutation analysis
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 11(14Q23.3) MUTATED    3  3
  DEL PEAK 11(14Q23.3) WILD-TYPE  6 13
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             6                             19 
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                             3                             13 
$`DEL PEAK 11(14Q23.3) MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2MS TCGA-FS-A1ZA 
       48.76        33.73        25.87        24.43       136.44        27.68 

$`DEL PEAK 11(14Q23.3) WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       20.38        68.09        29.82        14.70         2.56        18.58 
TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       43.23       101.95        14.30       204.62        96.23        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       26.73        26.37        20.91        74.73        27.02         0.20 
TCGA-GN-A266 
       10.09 

  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                         24.43                           0.20 
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                        136.44                         204.62 
  DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE 
                        30.705                         26.730 
[1] "24.4 - 136.4 (30.7)" "0.2 - 204.6 (26.7)" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK 11(14Q23.3) MUTATED"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK 11(14Q23.3) WILD-TYPE"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-GN-A266 
"DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK 11(14Q23.3) MUTATED"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK 11(14Q23.3) WILD-TYPE"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-GN-A266 
"DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
  "DEL PEAK 11(14Q23.3) MUTATED"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
"DEL PEAK 11(14Q23.3) WILD-TYPE"   "DEL PEAK 11(14Q23.3) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 11(14Q23.3) MUTATED" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 11(14Q23.3) WILD-TYPE" "DEL PEAK 11(14Q23.3) WILD-TYPE" 
                    TCGA-GN-A266 
"DEL PEAK 11(14Q23.3) WILD-TYPE" 
[1] "hr=" "1.5"
D18V2, continuous
                                vv
clus                             DISTANT METASTASIS
  DEL PEAK 11(14Q23.3) MUTATED                    3
  DEL PEAK 11(14Q23.3) WILD-TYPE                  4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 11(14Q23.3) MUTATED                                                                                          0
  DEL PEAK 11(14Q23.3) WILD-TYPE                                                                                        5
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 11(14Q23.3) MUTATED                     3
  DEL PEAK 11(14Q23.3) WILD-TYPE                  10
D18V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 11(14Q23.3) MUTATED
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            0
  REGIONAL LYMPH NODE                                                                                                 3
                                                                                          clus
vv                                                                                         DEL PEAK 11(14Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              5
  REGIONAL LYMPH NODE                                                                                                  10
D18V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 11(14Q23.3) MUTATED      2    4
  DEL PEAK 11(14Q23.3) WILD-TYPE    6   13
        clus
vv       DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE
  FEMALE                            2                              6
  MALE                              4                             13
                                vv
clus                             N0 N1B N2C N3
  DEL PEAK 11(14Q23.3) MUTATED    3   2   1  0
  DEL PEAK 11(14Q23.3) WILD-TYPE 13   1   1  2
D18V5, multiclass
     clus
vv    DEL PEAK 11(14Q23.3) MUTATED DEL PEAK 11(14Q23.3) WILD-TYPE
  N0                             3                             13
  N1B                            2                              1
  N2C                            1                              1
  N3                             0                              2
D18V6, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK 11(14Q23.3) MUTATED          1        0        2         0
  DEL PEAK 11(14Q23.3) WILD-TYPE        2        1        4         3
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(14Q23.3) MUTATED            2          1        0
  DEL PEAK 11(14Q23.3) WILD-TYPE          1          3        1
D18V7, multiclass

Clustering(19) Variable = Del Peak 12(16q12.1) mutation analysis
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(16Q12.1) MUTATED    6  6
  DEL PEAK 12(16Q12.1) WILD-TYPE  3 10
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                            12                             13 
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                             6                             10 
$`DEL PEAK 12(16Q12.1) MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GO 
       48.76        33.73         2.56        18.58        43.23       101.95 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FW-A3I3 
       96.23       136.44        26.73        27.68        74.73         0.20 

$`DEL PEAK 12(16Q12.1) WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2A2 
       20.38        68.09        29.82        14.70        25.87        24.43 
TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZZ 
       14.30       204.62        41.59        26.37        20.91        27.02 
TCGA-GN-A266 
       10.09 

  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                          0.20                          10.09 
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                        136.44                         204.62 
  DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE 
                         38.48                          25.87 
[1] "0.2 - 136.4 (38.5)"  "10.1 - 204.6 (25.9)"
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-D3-A2JF                     TCGA-DA-A1I0 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-DA-A1IC                     TCGA-EE-A17X 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A181                     TCGA-EE-A182 
  "DEL PEAK 12(16Q12.1) MUTATED" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A29L                     TCGA-EE-A29N 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A29V                     TCGA-EE-A2A2 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2GC                     TCGA-EE-A2GO 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2GR                     TCGA-EE-A2MI 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-EE-A2MJ                     TCGA-EE-A2MS 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-EE-A2MT                     TCGA-EE-A3AE 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-ER-A19F                     TCGA-FS-A1Z3 
"DEL PEAK 12(16Q12.1) WILD-TYPE" "DEL PEAK 12(16Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZA                     TCGA-FS-A1ZP 
  "DEL PEAK 12(16Q12.1) MUTATED"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-FS-A1ZZ                     TCGA-FW-A3I3 
"DEL PEAK 12(16Q12.1) WILD-TYPE"   "DEL PEAK 12(16Q12.1) MUTATED" 
                    TCGA-GN-A266 
"DEL PEAK 12(16Q12.1) WILD-TYPE" 
[1] "hr=" "2.2"
D19V2, continuous
                                vv
clus                             DISTANT METASTASIS
  DEL PEAK 12(16Q12.1) MUTATED                    3
  DEL PEAK 12(16Q12.1) WILD-TYPE                  4
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 12(16Q12.1) MUTATED                                                                                          1
  DEL PEAK 12(16Q12.1) WILD-TYPE                                                                                        4
                                vv
clus                             REGIONAL LYMPH NODE
  DEL PEAK 12(16Q12.1) MUTATED                     8
  DEL PEAK 12(16Q12.1) WILD-TYPE                   5
D19V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 12(16Q12.1) MUTATED
  DISTANT METASTASIS                                                                                                  3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
  REGIONAL LYMPH NODE                                                                                                 8
                                                                                          clus
vv                                                                                         DEL PEAK 12(16Q12.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              4
  REGIONAL LYMPH NODE                                                                                                   5
D19V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(16Q12.1) MUTATED      5    7
  DEL PEAK 12(16Q12.1) WILD-TYPE    3   10
        clus
vv       DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  FEMALE                            5                              3
  MALE                              7                             10
                                vv
clus                             N0 N1B N2C N3
  DEL PEAK 12(16Q12.1) MUTATED   10   0   1  1
  DEL PEAK 12(16Q12.1) WILD-TYPE  6   3   1  1
D19V5, multiclass
     clus
vv    DEL PEAK 12(16Q12.1) MUTATED DEL PEAK 12(16Q12.1) WILD-TYPE
  N0                            10                              6
  N1B                            0                              3
  N2C                            1                              1
  N3                             1                              1
D19V6, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE II STAGE IIB
  DEL PEAK 12(16Q12.1) MUTATED          2        0        5         1
  DEL PEAK 12(16Q12.1) WILD-TYPE        1        1        1         2
                                vv
clus                             STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(16Q12.1) MUTATED            1          1        1
  DEL PEAK 12(16Q12.1) WILD-TYPE          2          3        0
D19V7, 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")
