
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/403953/all_lesions.conf_99.cnv.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Primary/3180571/SKCM-All_Primary.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_Primary", "-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-All_Primary"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=31, in cluster file=46, common to both=29
[1] "Reduce the number of clustering variables from 20 to 19."
[1] 19 29
[1] "Amp Peak 1(5p15.33) mutation analysis"
[1] 3
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                            7                            22 
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                            7                            22 
[1] "Amp Peak 2(8q24.3) mutation analysis"
[1] 3
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                          14                           15 
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                          14                           15 
[1] "Amp Peak 4(13q31.3) mutation analysis"
[1] 3
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                           10                            19 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                           10                            19 
[1] "Del Peak  1(1p22.1) mutation analysis"
[1] 3
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            6                            23 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            6                            23 
[1] "Del Peak  2(1q41) mutation analysis"
[1] 3
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          5                          24 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          5                          24 
[1] "Del Peak  3(4q34.3) mutation analysis"
[1] 3
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                            8                            21 
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                            8                            21 
[1] "Del Peak  4(5q31.3) mutation analysis"
[1] 3
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                            9                            20 
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                            9                            20 
[1] "Del Peak  5(6q14.1) mutation analysis"
[1] 3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                           10                            19 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                           10                            19 
[1] "Del Peak  6(6q27) mutation analysis"
[1] 3
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                         13                          16 
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                         13                          16 
[1] "Del Peak  7(6q27) mutation analysis"
[1] 3
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                         13                          16 
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                         13                          16 
[1] "Del Peak  8(9p24.2) mutation analysis"
[1] 3
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                           20                             9 
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                           20                             9 
[1] "Del Peak  9(9p21.3) mutation analysis"
[1] 3
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                           23                             6 
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                           23                             6 
[1] "Del Peak 10(10p15.3) mutation analysis"
[1] 3
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                            17                             12 
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                            17                             12 
[1] "Del Peak 11(10q23.31) mutation analysis"
[1] 3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                             19                              10 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                             19                              10 
[1] "Del Peak 12(11q24.3) mutation analysis"
[1] 3
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                            14                             15 
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                            14                             15 
[1] "Del Peak 13(12q24.32) mutation analysis"
[1] 3
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                              9                              20 
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                              9                              20 
[1] "Del Peak 14(15q15.1) mutation analysis"
[1] 3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             7                             22 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             7                             22 
[1] "Del Peak 15(16q23.3) mutation analysis"
[1] 3
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                             8                             21 
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                             8                             21 
[1] "Del Peak 16(22q12.1) mutation analysis"
[1] 3
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                             4                             25 
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                             4                             25 
[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 29 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 
         237          118           16           13           41           NA 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF 
          39           36            9           NA           NA            4 
TCGA-EB-A3Y6 TCGA-EB-A3Y7 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z 
          16           NA            8            3            6           12 
TCGA-EB-A430 TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
          NA           NA          307           NA            1           NA 
TCGA-GN-A269 TCGA-GN-A26C TCGA-HR-A2OG TCGA-HR-A2OH TCGA-IH-A3EA 
          NA           NA           NA           NA          524 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=3,	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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=5,	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
T2A T3A T3B  T4 T4A T4B 
  1   2   1   1   1  22 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 29 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=8, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE

Clustering(1) Variable = Amp Peak 1(5p15.33) mutation analysis
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 1(5P15.33) MUTATED    6  0
  AMP PEAK 1(5P15.33) WILD-TYPE 11  5
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                            6                            16 
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                            0                             5 
$`AMP PEAK 1(5P15.33) MUTATED`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3Y6 TCGA-EB-A42Y 
        7.79         0.53         1.35         1.28         0.53         0.20 

$`AMP PEAK 1(5P15.33) WILD-TYPE`
TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A 
        3.88         0.43         1.18         0.30         0.13         0.26 
TCGA-EB-A41B TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GF-A2C7 
        0.10         0.39        12.10        10.09        24.00         0.03 
TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       15.35         5.59        26.99        17.23 

  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                         0.20                          0.03 
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                         7.79                         26.99 
  AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE 
                        0.905                         2.530 
[1] "0.2 - 7.8 (0.9)"  "0.0 - 27.0 (2.5)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 1(5P15.33) MUTATED"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 1(5P15.33) WILD-TYPE"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 1(5P15.33) MUTATED"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 1(5P15.33) WILD-TYPE"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 1(5P15.33) MUTATED"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 1(5P15.33) WILD-TYPE"   "AMP PEAK 1(5P15.33) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "AMP PEAK 1(5P15.33) MUTATED" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 1(5P15.33) WILD-TYPE" "AMP PEAK 1(5P15.33) WILD-TYPE" 
[1] "hr="     "8.1e+07"
D1V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 1(5P15.33) MUTATED                    0             6
  AMP PEAK 1(5P15.33) WILD-TYPE                  2            19
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 1(5P15.33) MUTATED                                                                                          1
  AMP PEAK 1(5P15.33) WILD-TYPE                                                                                        1
D1V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 1(5P15.33) MUTATED
  DISTANT METASTASIS                                                                                                 0
  PRIMARY TUMOR                                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
                                                                                          clus
vv                                                                                         AMP PEAK 1(5P15.33) WILD-TYPE
  DISTANT METASTASIS                                                                                                   2
  PRIMARY TUMOR                                                                                                       19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
D1V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 1(5P15.33) MUTATED      3    4
  AMP PEAK 1(5P15.33) WILD-TYPE    6   16
        clus
vv       AMP PEAK 1(5P15.33) MUTATED AMP PEAK 1(5P15.33) WILD-TYPE
  FEMALE                           3                             6
  MALE                             4                            16
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 1(5P15.33) MUTATED    5   0   0   0   2   0  0  0
  AMP PEAK 1(5P15.33) WILD-TYPE 10   1   1   1   1   1  3  3
D1V5, multiclass
D1V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  AMP PEAK 1(5P15.33) MUTATED          0        0         1         4
  AMP PEAK 1(5P15.33) WILD-TYPE        1        1         0        11
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 1(5P15.33) MUTATED            0          1          0        0
  AMP PEAK 1(5P15.33) WILD-TYPE          1          2          4        1
D1V7, multiclass

Clustering(2) Variable = Amp Peak 2(8q24.3) mutation analysis
D2V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 2(8Q24.3) MUTATED   11  2
  AMP PEAK 2(8Q24.3) WILD-TYPE  6  3
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                          13                            9 
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                           2                            3 
$`AMP PEAK 2(8Q24.3) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3XF 
        3.88         0.53         0.43         1.35         1.18         0.13 
TCGA-EB-A3Y6 TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 
        0.53         0.20         0.39        12.10        24.00         0.03 
TCGA-IH-A3EA 
       17.23 

$`AMP PEAK 2(8Q24.3) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A3HV TCGA-EB-A3XC TCGA-EB-A41A TCGA-EB-A41B TCGA-FR-A3R1 
        7.79         1.28         0.30         0.26         0.10        10.09 
TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C 
       15.35         5.59        26.99 

  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                        0.03                         0.10 
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                       24.00                        26.99 
  AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE 
                        0.53                         5.59 
[1] "0.0 - 24.0 (0.5)" "0.1 - 27.0 (5.6)"
                  TCGA-D9-A1X3                   TCGA-D9-A3Z4 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A1NK                   TCGA-EB-A24C 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A24D                   TCGA-EB-A3HV 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XB                   TCGA-EB-A3XC 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XF                   TCGA-EB-A3Y6 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A41A                   TCGA-EB-A41B 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A42Y                   TCGA-EB-A42Z 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-FR-A2OS                   TCGA-FR-A3R1 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-FS-A1ZN                   TCGA-GF-A2C7 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-GN-A263                   TCGA-GN-A269 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-IH-A3EA 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-D9-A1X3                   TCGA-D9-A3Z4 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A1NK                   TCGA-EB-A24C 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A24D                   TCGA-EB-A3HV 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XB                   TCGA-EB-A3XC 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XF                   TCGA-EB-A3Y6 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A41A                   TCGA-EB-A41B 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A42Y                   TCGA-EB-A42Z 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-FR-A2OS                   TCGA-FR-A3R1 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-FS-A1ZN                   TCGA-GF-A2C7 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-GN-A263                   TCGA-GN-A269 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-IH-A3EA 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-D9-A1X3                   TCGA-D9-A3Z4 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A1NK                   TCGA-EB-A24C 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A24D                   TCGA-EB-A3HV 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XB                   TCGA-EB-A3XC 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A3XF                   TCGA-EB-A3Y6 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-EB-A41A                   TCGA-EB-A41B 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-EB-A42Y                   TCGA-EB-A42Z 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-FR-A2OS                   TCGA-FR-A3R1 
  "AMP PEAK 2(8Q24.3) MUTATED" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-FS-A1ZN                   TCGA-GF-A2C7 
  "AMP PEAK 2(8Q24.3) MUTATED"   "AMP PEAK 2(8Q24.3) MUTATED" 
                  TCGA-GN-A263                   TCGA-GN-A269 
"AMP PEAK 2(8Q24.3) WILD-TYPE" "AMP PEAK 2(8Q24.3) WILD-TYPE" 
                  TCGA-GN-A26C                   TCGA-IH-A3EA 
"AMP PEAK 2(8Q24.3) WILD-TYPE"   "AMP PEAK 2(8Q24.3) MUTATED" 
[1] "hr=" "1"  
D2V2, continuous
                              vv
clus                           DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 2(8Q24.3) MUTATED                    1            12
  AMP PEAK 2(8Q24.3) WILD-TYPE                  1            13
                              vv
clus                           REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 2(8Q24.3) MUTATED                                                                                          1
  AMP PEAK 2(8Q24.3) WILD-TYPE                                                                                        1
D2V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 2(8Q24.3) MUTATED
  DISTANT METASTASIS                                                                                                1
  PRIMARY TUMOR                                                                                                    12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                          1
                                                                                          clus
vv                                                                                         AMP PEAK 2(8Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                  1
  PRIMARY TUMOR                                                                                                      13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
D2V4, binary
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(8Q24.3) MUTATED      4   10
  AMP PEAK 2(8Q24.3) WILD-TYPE    5   10
        clus
vv       AMP PEAK 2(8Q24.3) MUTATED AMP PEAK 2(8Q24.3) WILD-TYPE
  FEMALE                          4                            5
  MALE                           10                           10
                              vv
clus                           N0 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 2(8Q24.3) MUTATED    7   1   1   1   1   0  1  2
  AMP PEAK 2(8Q24.3) WILD-TYPE  8   0   0   0   2   1  2  1
D2V5, multiclass
D2V6, continuous
                              vv
clus                           STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA
  AMP PEAK 2(8Q24.3) MUTATED          0        1         0         8          1
  AMP PEAK 2(8Q24.3) WILD-TYPE        1        0         1         7          0
                              vv
clus                           STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 2(8Q24.3) MUTATED            2          2        0
  AMP PEAK 2(8Q24.3) WILD-TYPE          1          2        1
D2V7, multiclass

Clustering(3) Variable = Amp Peak 4(13q31.3) mutation analysis
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 4(13Q31.3) MUTATED    6  1
  AMP PEAK 4(13Q31.3) WILD-TYPE 11  4
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            7                            15 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                            1                             4 
$`AMP PEAK 4(13Q31.3) MUTATED`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A41B 
        7.79         3.88         0.43         1.35         1.28         0.10 
TCGA-GN-A269 
        5.59 

$`AMP PEAK 4(13Q31.3) WILD-TYPE`
TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A 
        0.53         1.18         0.30         0.13         0.53         0.26 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GF-A2C7 
        0.20         0.39        12.10        10.09        24.00         0.03 
TCGA-GN-A263 TCGA-GN-A26C TCGA-IH-A3EA 
       15.35        26.99        17.23 

  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                         0.10                          0.03 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                         7.79                         26.99 
  AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE 
                         1.35                          0.53 
[1] "0.1 - 7.8 (1.4)"  "0.0 - 27.0 (0.5)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "AMP PEAK 4(13Q31.3) MUTATED"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"AMP PEAK 4(13Q31.3) WILD-TYPE"   "AMP PEAK 4(13Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"AMP PEAK 4(13Q31.3) WILD-TYPE" "AMP PEAK 4(13Q31.3) WILD-TYPE" 
[1] "hr="     "1.4e+09"
D3V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  AMP PEAK 4(13Q31.3) MUTATED                    1             8
  AMP PEAK 4(13Q31.3) WILD-TYPE                  1            17
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  AMP PEAK 4(13Q31.3) MUTATED                                                                                          1
  AMP PEAK 4(13Q31.3) WILD-TYPE                                                                                        1
D3V3, multiclass
                                                                                          clus
vv                                                                                         AMP PEAK 4(13Q31.3) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
                                                                                          clus
vv                                                                                         AMP PEAK 4(13Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                       17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
D3V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(13Q31.3) MUTATED      3    7
  AMP PEAK 4(13Q31.3) WILD-TYPE    6   13
        clus
vv       AMP PEAK 4(13Q31.3) MUTATED AMP PEAK 4(13Q31.3) WILD-TYPE
  FEMALE                           3                             6
  MALE                             7                            13
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  AMP PEAK 4(13Q31.3) MUTATED    4   0   0   0   2   0  2  1
  AMP PEAK 4(13Q31.3) WILD-TYPE 11   1   1   1   1   1  1  2
D3V5, multiclass
D3V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  AMP PEAK 4(13Q31.3) MUTATED          1        0         1         3
  AMP PEAK 4(13Q31.3) WILD-TYPE        0        1         0        12
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMP PEAK 4(13Q31.3) MUTATED            0          1          2        0
  AMP PEAK 4(13Q31.3) WILD-TYPE          1          2          2        1
D3V7, multiclass

Clustering(4) Variable = Del Peak  1(1p22.1) mutation analysis
D4V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  1(1P22.1) MUTATED    4  0
  DEL PEAK  1(1P22.1) WILD-TYPE 13  5
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            4                            18 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            0                             5 
$`DEL PEAK  1(1P22.1) MUTATED`
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3Y6 
        0.43         1.35         1.28         0.53 

$`DEL PEAK  1(1P22.1) WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        7.79         3.88         0.53         1.18         0.30         0.13 
TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 
        0.26         0.10         0.20         0.39        12.10        10.09 
TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       24.00         0.03        15.35         5.59        26.99        17.23 

  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                         0.43                          0.03 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                         1.35                         26.99 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                        0.905                         2.530 
[1] "0.4 - 1.4 (0.9)"  "0.0 - 27.0 (2.5)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  1(1P22.1) MUTATED"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  1(1P22.1) MUTATED"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  1(1P22.1) MUTATED"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  1(1P22.1) WILD-TYPE"   "DEL PEAK  1(1P22.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  1(1P22.1) WILD-TYPE" "DEL PEAK  1(1P22.1) WILD-TYPE" 
[1] "hr=" NA   
D4V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  1(1P22.1) MUTATED                    1             5
  DEL PEAK  1(1P22.1) WILD-TYPE                  1            20
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  1(1P22.1) MUTATED                                                                                          0
  DEL PEAK  1(1P22.1) WILD-TYPE                                                                                        2
D4V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P22.1) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           0
                                                                                          clus
vv                                                                                         DEL PEAK  1(1P22.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                       20
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
D4V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      3    3
  DEL PEAK  1(1P22.1) WILD-TYPE    6   17
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  FEMALE                           3                             6
  MALE                             3                            17
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  1(1P22.1) MUTATED    2   0   0   1   1   1  0  1
  DEL PEAK  1(1P22.1) WILD-TYPE 13   1   1   0   2   0  3  2
D4V5, multiclass
D4V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  1(1P22.1) MUTATED          0        0         0         3
  DEL PEAK  1(1P22.1) WILD-TYPE        1        1         1        12
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  1(1P22.1) MUTATED            0          3          0        0
  DEL PEAK  1(1P22.1) WILD-TYPE          1          0          4        1
D4V7, multiclass

Clustering(5) Variable = Del Peak  2(1q41) mutation analysis
D5V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1Q41) MUTATED    5  0
  DEL PEAK  2(1Q41) WILD-TYPE 12  5
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          5                          17 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                          0                           5 
$`DEL PEAK  2(1Q41) MUTATED`
TCGA-D9-A1X3 TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Z TCGA-IH-A3EA 
        7.79         0.53         0.10         0.39        17.23 

$`DEL PEAK  2(1Q41) WILD-TYPE`
TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        3.88         0.53         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A42Y TCGA-FR-A2OS TCGA-FR-A3R1 
        0.30         0.13         0.26         0.20        12.10        10.09 
TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C 
       24.00         0.03        15.35         5.59        26.99 

  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                       0.10                        0.03 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                      17.23                       26.99 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                       0.53                        1.28 
[1] "0.1 - 17.2 (0.5)" "0.0 - 27.0 (1.3)"
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
  "DEL PEAK  2(1Q41) MUTATED" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
  "DEL PEAK  2(1Q41) MUTATED" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
  "DEL PEAK  2(1Q41) MUTATED" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  2(1Q41) WILD-TYPE" "DEL PEAK  2(1Q41) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  2(1Q41) WILD-TYPE"   "DEL PEAK  2(1Q41) MUTATED" 
[1] "hr="     "7.5e+08"
D5V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  2(1Q41) MUTATED                    0             4
  DEL PEAK  2(1Q41) WILD-TYPE                  2            21
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  2(1Q41) MUTATED                                                                                          1
  DEL PEAK  2(1Q41) WILD-TYPE                                                                                        1
D5V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  2(1Q41) MUTATED
  DISTANT METASTASIS                                                                                               0
  PRIMARY TUMOR                                                                                                    4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         1
                                                                                          clus
vv                                                                                         DEL PEAK  2(1Q41) WILD-TYPE
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                     21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
D5V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      2    3
  DEL PEAK  2(1Q41) WILD-TYPE    7   17
        clus
vv       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  FEMALE                         2                           7
  MALE                           3                          17
                             vv
clus                          N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  2(1Q41) MUTATED    3   0   1   0   1   0  0  0
  DEL PEAK  2(1Q41) WILD-TYPE 12   1   0   1   2   1  3  3
D5V5, multiclass
D5V6, continuous
                             vv
clus                          STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA
  DEL PEAK  2(1Q41) MUTATED          0        0         0         3          0
  DEL PEAK  2(1Q41) WILD-TYPE        1        1         1        12          1
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  2(1Q41) MUTATED            0          1        0
  DEL PEAK  2(1Q41) WILD-TYPE          3          3        1
D5V7, multiclass

Clustering(6) Variable = Del Peak  3(4q34.3) mutation analysis
D6V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(4Q34.3) MUTATED    5  0
  DEL PEAK  3(4Q34.3) WILD-TYPE 12  5
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                            5                            17 
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                            0                             5 
$`DEL PEAK  3(4Q34.3) MUTATED`
TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A41B 
        0.43         1.28         1.18         0.30         0.10 

$`DEL PEAK  3(4Q34.3) WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24D TCGA-EB-A3XF TCGA-EB-A3Y6 
        7.79         3.88         0.53         1.35         0.13         0.53 
TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN 
        0.26         0.20         0.39        12.10        10.09        24.00 
TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        0.03        15.35         5.59        26.99        17.23 

  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                         1.28                         26.99 
  DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE 
                         0.43                          3.88 
[1] "0.1 - 1.3 (0.4)"  "0.0 - 27.0 (3.9)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  3(4Q34.3) MUTATED"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  3(4Q34.3) MUTATED"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  3(4Q34.3) MUTATED"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  3(4Q34.3) WILD-TYPE"   "DEL PEAK  3(4Q34.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  3(4Q34.3) WILD-TYPE" "DEL PEAK  3(4Q34.3) WILD-TYPE" 
[1] "hr=" NA   
D6V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  3(4Q34.3) MUTATED                    1             7
  DEL PEAK  3(4Q34.3) WILD-TYPE                  1            18
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  3(4Q34.3) MUTATED                                                                                          0
  DEL PEAK  3(4Q34.3) WILD-TYPE                                                                                        2
D6V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  3(4Q34.3) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           0
                                                                                          clus
vv                                                                                         DEL PEAK  3(4Q34.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                       18
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
D6V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(4Q34.3) MUTATED      3    5
  DEL PEAK  3(4Q34.3) WILD-TYPE    6   15
        clus
vv       DEL PEAK  3(4Q34.3) MUTATED DEL PEAK  3(4Q34.3) WILD-TYPE
  FEMALE                           3                             6
  MALE                             5                            15
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  3(4Q34.3) MUTATED    4   0   0   1   0   1  0  2
  DEL PEAK  3(4Q34.3) WILD-TYPE 11   1   1   0   3   0  3  1
D6V5, multiclass
D6V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  3(4Q34.3) MUTATED          0        1         0         5
  DEL PEAK  3(4Q34.3) WILD-TYPE        1        0         1        10
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  3(4Q34.3) MUTATED            0          2          0        0
  DEL PEAK  3(4Q34.3) WILD-TYPE          1          1          4        1
D6V7, multiclass

Clustering(7) Variable = Del Peak  4(5q31.3) mutation analysis
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(5Q31.3) MUTATED    5  2
  DEL PEAK  4(5Q31.3) WILD-TYPE 12  3
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                            7                            15 
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                            2                             3 
$`DEL PEAK  4(5Q31.3) MUTATED`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A3XC TCGA-EB-A3XF TCGA-GN-A263 
        7.79         3.88         0.43         0.30         0.13        15.35 
TCGA-GN-A269 
        5.59 

$`DEL PEAK  4(5Q31.3) WILD-TYPE`
TCGA-EB-A1NK TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3Y6 TCGA-EB-A41A 
        0.53         1.35         1.28         1.18         0.53         0.26 
TCGA-EB-A41B TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN 
        0.10         0.20         0.39        12.10        10.09        24.00 
TCGA-GF-A2C7 TCGA-GN-A26C TCGA-IH-A3EA 
        0.03        26.99        17.23 

  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                        15.35                         26.99 
  DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE 
                         3.88                          1.18 
[1] "0.1 - 15.3 (3.9)" "0.0 - 27.0 (1.2)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  4(5Q31.3) MUTATED" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  4(5Q31.3) MUTATED" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
"DEL PEAK  4(5Q31.3) WILD-TYPE"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  4(5Q31.3) MUTATED" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  4(5Q31.3) MUTATED"   "DEL PEAK  4(5Q31.3) MUTATED" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  4(5Q31.3) WILD-TYPE" "DEL PEAK  4(5Q31.3) WILD-TYPE" 
[1] "hr=" "5.6"
D7V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  4(5Q31.3) MUTATED                    2             6
  DEL PEAK  4(5Q31.3) WILD-TYPE                  0            19
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  4(5Q31.3) MUTATED                                                                                          1
  DEL PEAK  4(5Q31.3) WILD-TYPE                                                                                        1
D7V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  4(5Q31.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                      6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
                                                                                          clus
vv                                                                                         DEL PEAK  4(5Q31.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   0
  PRIMARY TUMOR                                                                                                       19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
D7V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(5Q31.3) MUTATED      2    7
  DEL PEAK  4(5Q31.3) WILD-TYPE    7   13
        clus
vv       DEL PEAK  4(5Q31.3) MUTATED DEL PEAK  4(5Q31.3) WILD-TYPE
  FEMALE                           2                             7
  MALE                             7                            13
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  4(5Q31.3) MUTATED    2   0   0   1   1   0  3  1
  DEL PEAK  4(5Q31.3) WILD-TYPE 13   1   1   0   2   1  0  2
D7V5, multiclass
D7V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  4(5Q31.3) MUTATED          0        0         0         3
  DEL PEAK  4(5Q31.3) WILD-TYPE        1        1         1        12
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  4(5Q31.3) MUTATED            0          1          2        1
  DEL PEAK  4(5Q31.3) WILD-TYPE          1          2          2        0
D7V7, multiclass

Clustering(8) Variable = Del Peak  5(6q14.1) mutation analysis
D8V1, survival
                               sevent
clus2                           0 1
  DEL PEAK  5(6Q14.1) MUTATED   8 0
  DEL PEAK  5(6Q14.1) WILD-TYPE 9 5
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            8                            14 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            0                             5 
$`DEL PEAK  5(6Q14.1) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        3.88         1.35         1.18         0.30         0.13         0.53 
TCGA-GF-A2C7 TCGA-IH-A3EA 
        0.03        17.23 

$`DEL PEAK  5(6Q14.1) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A41A TCGA-EB-A41B 
        7.79         0.53         0.43         1.28         0.26         0.10 
TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GN-A263 
        0.20         0.39        12.10        10.09        24.00        15.35 
TCGA-GN-A269 TCGA-GN-A26C 
        5.59        26.99 

  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                        17.23                         26.99 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                        0.855                         3.435 
[1] "0.0 - 17.2 (0.9)" "0.1 - 27.0 (3.4)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  5(6Q14.1) MUTATED" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  5(6Q14.1) MUTATED"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
"DEL PEAK  5(6Q14.1) WILD-TYPE" "DEL PEAK  5(6Q14.1) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  5(6Q14.1) WILD-TYPE"   "DEL PEAK  5(6Q14.1) MUTATED" 
[1] "hr="     "2.6e+08"
D8V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  5(6Q14.1) MUTATED                    1             8
  DEL PEAK  5(6Q14.1) WILD-TYPE                  1            17
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  5(6Q14.1) MUTATED                                                                                          1
  DEL PEAK  5(6Q14.1) WILD-TYPE                                                                                        1
D8V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  5(6Q14.1) MUTATED
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                      8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
                                                                                          clus
vv                                                                                         DEL PEAK  5(6Q14.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                       17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
D8V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      2    8
  DEL PEAK  5(6Q14.1) WILD-TYPE    7   12
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  FEMALE                           2                             7
  MALE                             8                            12
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  5(6Q14.1) MUTATED    6   0   0   0   1   0  1  1
  DEL PEAK  5(6Q14.1) WILD-TYPE  9   1   1   1   2   1  2  2
D8V5, multiclass
D8V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  5(6Q14.1) MUTATED          0        1         0         6
  DEL PEAK  5(6Q14.1) WILD-TYPE        1        0         1         9
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  5(6Q14.1) MUTATED            0          1          1        0
  DEL PEAK  5(6Q14.1) WILD-TYPE          1          2          3        1
D8V7, multiclass

Clustering(9) Variable = Del Peak  6(6q27) mutation analysis
D9V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  6(6Q27) MUTATED   8 1
  DEL PEAK  6(6Q27) WILD-TYPE 9 4
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                          9                          13 
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                          1                           4 
$`DEL PEAK  6(6Q27) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        3.88         1.35         1.18         0.30         0.13         0.53 
TCGA-EB-A42Z TCGA-FS-A1ZN TCGA-IH-A3EA 
        0.39        24.00        17.23 

$`DEL PEAK  6(6Q27) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A41A TCGA-EB-A41B 
        7.79         0.53         0.43         1.28         0.26         0.10 
TCGA-EB-A42Y TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 
        0.20        12.10        10.09         0.03        15.35         5.59 
TCGA-GN-A26C 
       26.99 

  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                       0.13                        0.03 
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                      24.00                       26.99 
  DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE 
                       1.18                        1.28 
[1] "0.1 - 24.0 (1.2)" "0.0 - 27.0 (1.3)"
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  6(6Q27) MUTATED"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  6(6Q27) MUTATED" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  6(6Q27) WILD-TYPE" "DEL PEAK  6(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  6(6Q27) WILD-TYPE"   "DEL PEAK  6(6Q27) MUTATED" 
[1] "hr=" "2.2"
D9V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  6(6Q27) MUTATED                    1            12
  DEL PEAK  6(6Q27) WILD-TYPE                  1            13
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  6(6Q27) MUTATED                                                                                          0
  DEL PEAK  6(6Q27) WILD-TYPE                                                                                        2
D9V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  6(6Q27) MUTATED
  DISTANT METASTASIS                                                                                               1
  PRIMARY TUMOR                                                                                                   12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         0
                                                                                          clus
vv                                                                                         DEL PEAK  6(6Q27) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                     13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           2
D9V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q27) MUTATED      4    9
  DEL PEAK  6(6Q27) WILD-TYPE    5   11
        clus
vv       DEL PEAK  6(6Q27) MUTATED DEL PEAK  6(6Q27) WILD-TYPE
  FEMALE                         4                           5
  MALE                           9                          11
                             vv
clus                          N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  6(6Q27) MUTATED    5   1   1   0   1   1  1  2
  DEL PEAK  6(6Q27) WILD-TYPE 10   0   0   1   2   0  2  1
D9V5, multiclass
D9V6, continuous
                             vv
clus                          STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA
  DEL PEAK  6(6Q27) MUTATED          0        1         0         6          1
  DEL PEAK  6(6Q27) WILD-TYPE        1        0         1         9          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  6(6Q27) MUTATED            2          2        0
  DEL PEAK  6(6Q27) WILD-TYPE          1          2        1
D9V7, multiclass

Clustering(10) Variable = Del Peak  7(6q27) mutation analysis
D10V1, survival
                             sevent
clus2                         0 1
  DEL PEAK  7(6Q27) MUTATED   8 1
  DEL PEAK  7(6Q27) WILD-TYPE 9 4
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                          9                          13 
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                          1                           4 
$`DEL PEAK  7(6Q27) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 
        3.88         1.35         1.18         0.30         0.13         0.53 
TCGA-EB-A42Z TCGA-FS-A1ZN TCGA-IH-A3EA 
        0.39        24.00        17.23 

$`DEL PEAK  7(6Q27) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A41A TCGA-EB-A41B 
        7.79         0.53         0.43         1.28         0.26         0.10 
TCGA-EB-A42Y TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 
        0.20        12.10        10.09         0.03        15.35         5.59 
TCGA-GN-A26C 
       26.99 

  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                       0.13                        0.03 
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                      24.00                       26.99 
  DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE 
                       1.18                        1.28 
[1] "0.1 - 24.0 (1.2)" "0.0 - 27.0 (1.3)"
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-D9-A1X3                  TCGA-D9-A3Z4 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A1NK                  TCGA-EB-A24C 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A24D                  TCGA-EB-A3HV 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A3XB                  TCGA-EB-A3XC 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A3XF                  TCGA-EB-A3Y6 
  "DEL PEAK  7(6Q27) MUTATED"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-EB-A41A                  TCGA-EB-A41B 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-EB-A42Y                  TCGA-EB-A42Z 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
                 TCGA-FR-A2OS                  TCGA-FR-A3R1 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-FS-A1ZN                  TCGA-GF-A2C7 
  "DEL PEAK  7(6Q27) MUTATED" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A263                  TCGA-GN-A269 
"DEL PEAK  7(6Q27) WILD-TYPE" "DEL PEAK  7(6Q27) WILD-TYPE" 
                 TCGA-GN-A26C                  TCGA-IH-A3EA 
"DEL PEAK  7(6Q27) WILD-TYPE"   "DEL PEAK  7(6Q27) MUTATED" 
[1] "hr=" "2.2"
D10V2, continuous
                             vv
clus                          DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  7(6Q27) MUTATED                    1            12
  DEL PEAK  7(6Q27) WILD-TYPE                  1            13
                             vv
clus                          REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  7(6Q27) MUTATED                                                                                          0
  DEL PEAK  7(6Q27) WILD-TYPE                                                                                        2
D10V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  7(6Q27) MUTATED
  DISTANT METASTASIS                                                                                               1
  PRIMARY TUMOR                                                                                                   12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                         0
                                                                                          clus
vv                                                                                         DEL PEAK  7(6Q27) WILD-TYPE
  DISTANT METASTASIS                                                                                                 1
  PRIMARY TUMOR                                                                                                     13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           2
D10V4, binary
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(6Q27) MUTATED      4    9
  DEL PEAK  7(6Q27) WILD-TYPE    5   11
        clus
vv       DEL PEAK  7(6Q27) MUTATED DEL PEAK  7(6Q27) WILD-TYPE
  FEMALE                         4                           5
  MALE                           9                          11
                             vv
clus                          N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  7(6Q27) MUTATED    5   1   1   0   1   1  1  2
  DEL PEAK  7(6Q27) WILD-TYPE 10   0   0   1   2   0  2  1
D10V5, multiclass
D10V6, continuous
                             vv
clus                          STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA
  DEL PEAK  7(6Q27) MUTATED          0        1         0         6          1
  DEL PEAK  7(6Q27) WILD-TYPE        1        0         1         9          0
                             vv
clus                          STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  7(6Q27) MUTATED            2          2        0
  DEL PEAK  7(6Q27) WILD-TYPE          1          2        1
D10V7, multiclass

Clustering(11) Variable = Del Peak  8(9p24.2) mutation analysis
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(9P24.2) MUTATED   12  2
  DEL PEAK  8(9P24.2) WILD-TYPE  5  3
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                           14                             8 
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                            2                             3 
$`DEL PEAK  8(9P24.2) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        3.88         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z TCGA-FR-A2OS 
        0.13         0.53         0.26         0.10         0.39        12.10 
TCGA-GF-A2C7 TCGA-GN-A263 
        0.03        15.35 

$`DEL PEAK  8(9P24.2) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A42Y TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GN-A269 
        7.79         0.53         0.20        10.09        24.00         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       26.99        17.23 

  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                         0.03                          0.20 
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                        15.35                         26.99 
  DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE 
                         0.48                          8.94 
[1] "0.0 - 15.3 (0.5)" "0.2 - 27.0 (8.9)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  8(9P24.2) WILD-TYPE" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  8(9P24.2) WILD-TYPE" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  8(9P24.2) MUTATED"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
"DEL PEAK  8(9P24.2) WILD-TYPE"   "DEL PEAK  8(9P24.2) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  8(9P24.2) MUTATED" "DEL PEAK  8(9P24.2) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  8(9P24.2) WILD-TYPE" "DEL PEAK  8(9P24.2) WILD-TYPE" 
[1] "hr=" "4.9"
D11V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  8(9P24.2) MUTATED                    2            17
  DEL PEAK  8(9P24.2) WILD-TYPE                  0             8
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  8(9P24.2) MUTATED                                                                                          1
  DEL PEAK  8(9P24.2) WILD-TYPE                                                                                        1
D11V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  8(9P24.2) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                     17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           1
                                                                                          clus
vv                                                                                         DEL PEAK  8(9P24.2) WILD-TYPE
  DISTANT METASTASIS                                                                                                   0
  PRIMARY TUMOR                                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
D11V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(9P24.2) MUTATED      7   13
  DEL PEAK  8(9P24.2) WILD-TYPE    2    7
        clus
vv       DEL PEAK  8(9P24.2) MUTATED DEL PEAK  8(9P24.2) WILD-TYPE
  FEMALE                           7                             2
  MALE                            13                             7
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  8(9P24.2) MUTATED   11   0   1   1   1   0  2  3
  DEL PEAK  8(9P24.2) WILD-TYPE  4   1   0   0   2   1  1  0
D11V5, multiclass
D11V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  8(9P24.2) MUTATED          1        1         1        11
  DEL PEAK  8(9P24.2) WILD-TYPE        0        0         0         4
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  8(9P24.2) MUTATED            0          2          2        1
  DEL PEAK  8(9P24.2) WILD-TYPE          1          1          2        0
D11V7, multiclass

Clustering(12) Variable = Del Peak  9(9p21.3) mutation analysis
D12V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(9P21.3) MUTATED   14  3
  DEL PEAK  9(9P21.3) WILD-TYPE  3  2
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                           17                             5 
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                            3                             2 
$`DEL PEAK  9(9P21.3) MUTATED`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        7.79         3.88         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y 
        0.30         0.13         0.53         0.26         0.10         0.20 
TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.39        12.10        24.00         0.03        15.35 

$`DEL PEAK  9(9P21.3) WILD-TYPE`
TCGA-EB-A1NK TCGA-FR-A3R1 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        0.53        10.09         5.59        26.99        17.23 

  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                         0.03                          0.53 
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                        24.00                         26.99 
  DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE 
                         0.53                         10.09 
[1] "0.0 - 24.0 (0.5)"  "0.5 - 27.0 (10.1)"
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  9(9P21.3) WILD-TYPE"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  9(9P21.3) WILD-TYPE" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  9(9P21.3) WILD-TYPE"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  9(9P21.3) WILD-TYPE" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-D9-A1X3                    TCGA-D9-A3Z4 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A1NK                    TCGA-EB-A24C 
"DEL PEAK  9(9P21.3) WILD-TYPE"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A24D                    TCGA-EB-A3HV 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XB                    TCGA-EB-A3XC 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A3XF                    TCGA-EB-A3Y6 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A41A                    TCGA-EB-A41B 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-EB-A42Y                    TCGA-EB-A42Z 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-FR-A2OS                    TCGA-FR-A3R1 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-FS-A1ZN                    TCGA-GF-A2C7 
  "DEL PEAK  9(9P21.3) MUTATED"   "DEL PEAK  9(9P21.3) MUTATED" 
                   TCGA-GN-A263                    TCGA-GN-A269 
  "DEL PEAK  9(9P21.3) MUTATED" "DEL PEAK  9(9P21.3) WILD-TYPE" 
                   TCGA-GN-A26C                    TCGA-IH-A3EA 
"DEL PEAK  9(9P21.3) WILD-TYPE" "DEL PEAK  9(9P21.3) WILD-TYPE" 
[1] "hr=" "2.7"
D12V2, continuous
                               vv
clus                            DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK  9(9P21.3) MUTATED                    2            19
  DEL PEAK  9(9P21.3) WILD-TYPE                  0             6
                               vv
clus                            REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK  9(9P21.3) MUTATED                                                                                          2
  DEL PEAK  9(9P21.3) WILD-TYPE                                                                                        0
D12V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK  9(9P21.3) MUTATED
  DISTANT METASTASIS                                                                                                 2
  PRIMARY TUMOR                                                                                                     19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                           2
                                                                                          clus
vv                                                                                         DEL PEAK  9(9P21.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                   0
  PRIMARY TUMOR                                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             0
D12V4, binary
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(9P21.3) MUTATED      8   15
  DEL PEAK  9(9P21.3) WILD-TYPE    1    5
        clus
vv       DEL PEAK  9(9P21.3) MUTATED DEL PEAK  9(9P21.3) WILD-TYPE
  FEMALE                           8                             1
  MALE                            15                             5
                               vv
clus                            N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK  9(9P21.3) MUTATED   12   1   1   1   2   0  2  3
  DEL PEAK  9(9P21.3) WILD-TYPE  3   0   0   0   1   1  1  0
D12V5, multiclass
D12V6, continuous
                               vv
clus                            STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK  9(9P21.3) MUTATED          1        1         1        12
  DEL PEAK  9(9P21.3) WILD-TYPE        0        0         0         3
                               vv
clus                            STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK  9(9P21.3) MUTATED            1          2          2        1
  DEL PEAK  9(9P21.3) WILD-TYPE          0          1          2        0
D12V7, multiclass

Clustering(13) Variable = Del Peak 10(10p15.3) mutation analysis
D13V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(10P15.3) MUTATED   11  2
  DEL PEAK 10(10P15.3) WILD-TYPE  6  3
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                            13                              9 
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                             2                              3 
$`DEL PEAK 10(10P15.3) MUTATED`
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        7.79         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FS-A1ZN 
        0.13         0.53         0.20         0.39        12.10        24.00 
TCGA-GF-A2C7 
        0.03 

$`DEL PEAK 10(10P15.3) WILD-TYPE`
TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A41A TCGA-EB-A41B TCGA-FR-A3R1 TCGA-GN-A263 
        3.88         0.53         0.26         0.10        10.09        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                         24.00                          26.99 
  DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE 
                          0.53                           5.59 
[1] "0.0 - 24.0 (0.5)" "0.1 - 27.0 (5.6)"
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 10(10P15.3) WILD-TYPE"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 10(10P15.3) WILD-TYPE"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 10(10P15.3) WILD-TYPE"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
  "DEL PEAK 10(10P15.3) MUTATED" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
  "DEL PEAK 10(10P15.3) MUTATED"   "DEL PEAK 10(10P15.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 10(10P15.3) WILD-TYPE" "DEL PEAK 10(10P15.3) WILD-TYPE" 
[1] "hr=" "1.7"
D13V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 10(10P15.3) MUTATED                    2            13
  DEL PEAK 10(10P15.3) WILD-TYPE                  0            12
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 10(10P15.3) MUTATED                                                                                          2
  DEL PEAK 10(10P15.3) WILD-TYPE                                                                                        0
D13V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 10(10P15.3) MUTATED
  DISTANT METASTASIS                                                                                                  2
  PRIMARY TUMOR                                                                                                      13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            2
                                                                                          clus
vv                                                                                         DEL PEAK 10(10P15.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    0
  PRIMARY TUMOR                                                                                                        12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              0
D13V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(10P15.3) MUTATED      6   11
  DEL PEAK 10(10P15.3) WILD-TYPE    3    9
        clus
vv       DEL PEAK 10(10P15.3) MUTATED DEL PEAK 10(10P15.3) WILD-TYPE
  FEMALE                            6                              3
  MALE                             11                              9
                                vv
clus                             N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 10(10P15.3) MUTATED    8   1   1   1   2   0  0  3
  DEL PEAK 10(10P15.3) WILD-TYPE  7   0   0   0   1   1  3  0
D13V5, multiclass
D13V6, continuous
                                vv
clus                             STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 10(10P15.3) MUTATED          1        1         0         9
  DEL PEAK 10(10P15.3) WILD-TYPE        0        0         1         6
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 10(10P15.3) MUTATED            1          2          1        0
  DEL PEAK 10(10P15.3) WILD-TYPE          0          1          3        1
D13V7, multiclass

Clustering(14) Variable = Del Peak 11(10q23.31) mutation analysis
D14V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 11(10Q23.31) MUTATED   11  2
  DEL PEAK 11(10Q23.31) WILD-TYPE  6  3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                             13                               9 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              2                               3 
$`DEL PEAK 11(10Q23.31) MUTATED`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        7.79         3.88         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FS-A1ZN 
        0.30         0.13         0.53         0.39        12.10        24.00 
TCGA-GF-A2C7 
        0.03 

$`DEL PEAK 11(10Q23.31) WILD-TYPE`
TCGA-EB-A1NK TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Y TCGA-FR-A3R1 TCGA-GN-A263 
        0.53         0.26         0.10         0.20        10.09        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                          24.00                           26.99 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                           1.18                            5.59 
[1] "0.0 - 24.0 (1.2)" "0.1 - 27.0 (5.6)"
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 11(10Q23.31) WILD-TYPE"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
  "DEL PEAK 11(10Q23.31) MUTATED" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
  "DEL PEAK 11(10Q23.31) MUTATED"   "DEL PEAK 11(10Q23.31) MUTATED" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 11(10Q23.31) WILD-TYPE" "DEL PEAK 11(10Q23.31) WILD-TYPE" 
[1] "hr=" "1.7"
D14V2, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 11(10Q23.31) MUTATED                    2            15
  DEL PEAK 11(10Q23.31) WILD-TYPE                  0            10
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 11(10Q23.31) MUTATED                                                                                          2
  DEL PEAK 11(10Q23.31) WILD-TYPE                                                                                        0
D14V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 11(10Q23.31) MUTATED
  DISTANT METASTASIS                                                                                                   2
  PRIMARY TUMOR                                                                                                       15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             2
                                                                                          clus
vv                                                                                         DEL PEAK 11(10Q23.31) WILD-TYPE
  DISTANT METASTASIS                                                                                                     0
  PRIMARY TUMOR                                                                                                         10
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               0
D14V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      6   13
  DEL PEAK 11(10Q23.31) WILD-TYPE    3    7
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  FEMALE                             6                               3
  MALE                              13                               7
                                 vv
clus                              N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 11(10Q23.31) MUTATED    9   1   1   1   2   0  1  3
  DEL PEAK 11(10Q23.31) WILD-TYPE  6   0   0   0   1   1  2  0
D14V5, multiclass
D14V6, continuous
                                 vv
clus                              STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 11(10Q23.31) MUTATED          1        1         1         9
  DEL PEAK 11(10Q23.31) WILD-TYPE        0        0         0         6
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 11(10Q23.31) MUTATED            1          2          2        0
  DEL PEAK 11(10Q23.31) WILD-TYPE          0          1          2        1
D14V7, multiclass

Clustering(15) Variable = Del Peak 12(11q24.3) mutation analysis
D15V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(11Q24.3) MUTATED   11  0
  DEL PEAK 12(11Q24.3) WILD-TYPE  6  5
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                            11                             11 
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                             0                              5 
$`DEL PEAK 12(11Q24.3) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        3.88         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-EB-A42Z TCGA-FR-A3R1 TCGA-GF-A2C7 
        0.53         0.10         0.39        10.09         0.03 

$`DEL PEAK 12(11Q24.3) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A42Y TCGA-FR-A2OS 
        7.79         0.53         0.13         0.26         0.20        12.10 
TCGA-FS-A1ZN TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       24.00        15.35         5.59        26.99        17.23 

  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                          0.03                           0.13 
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                         10.09                          26.99 
  DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE 
                          0.53                           7.79 
[1] "0.0 - 10.1 (0.5)" "0.1 - 27.0 (7.8)"
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
  "DEL PEAK 12(11Q24.3) MUTATED"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 12(11Q24.3) WILD-TYPE"   "DEL PEAK 12(11Q24.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 12(11Q24.3) WILD-TYPE" "DEL PEAK 12(11Q24.3) WILD-TYPE" 
[1] "hr="     "8.1e+07"
D15V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 12(11Q24.3) MUTATED                    1            12
  DEL PEAK 12(11Q24.3) WILD-TYPE                  1            13
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 12(11Q24.3) MUTATED                                                                                          1
  DEL PEAK 12(11Q24.3) WILD-TYPE                                                                                        1
D15V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 12(11Q24.3) MUTATED
  DISTANT METASTASIS                                                                                                  1
  PRIMARY TUMOR                                                                                                      12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
                                                                                          clus
vv                                                                                         DEL PEAK 12(11Q24.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    1
  PRIMARY TUMOR                                                                                                        13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              1
D15V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(11Q24.3) MUTATED      4   10
  DEL PEAK 12(11Q24.3) WILD-TYPE    5   10
        clus
vv       DEL PEAK 12(11Q24.3) MUTATED DEL PEAK 12(11Q24.3) WILD-TYPE
  FEMALE                            4                              5
  MALE                             10                             10
                                vv
clus                             N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 12(11Q24.3) MUTATED    7   0   1   1   1   1  1  2
  DEL PEAK 12(11Q24.3) WILD-TYPE  8   1   0   0   2   0  2  1
D15V5, multiclass
D15V6, continuous
                                vv
clus                             STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 12(11Q24.3) MUTATED          0        1         0         8
  DEL PEAK 12(11Q24.3) WILD-TYPE        1        0         1         7
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 12(11Q24.3) MUTATED            0          3          2        0
  DEL PEAK 12(11Q24.3) WILD-TYPE          1          0          2        1
D15V7, multiclass

Clustering(16) Variable = Del Peak 13(12q24.32) mutation analysis
D16V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 13(12Q24.32) MUTATED    7  0
  DEL PEAK 13(12Q24.32) WILD-TYPE 10  5
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                              7                              15 
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                              0                               5 
$`DEL PEAK 13(12Q24.32) MUTATED`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3Y6 
        7.79         0.53         0.43         1.35         1.28         0.53 
TCGA-EB-A42Z 
        0.39 

$`DEL PEAK 13(12Q24.32) WILD-TYPE`
TCGA-D9-A3Z4 TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A41A TCGA-EB-A41B 
        3.88         1.18         0.30         0.13         0.26         0.10 
TCGA-EB-A42Y TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.20        12.10        10.09        24.00         0.03        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                           0.39                            0.03 
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                           7.79                           26.99 
  DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE 
                           0.53                            3.88 
[1] "0.4 - 7.8 (0.5)"  "0.0 - 27.0 (3.9)"
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 13(12Q24.32) MUTATED" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 13(12Q24.32) MUTATED" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-D9-A1X3                      TCGA-D9-A3Z4 
  "DEL PEAK 13(12Q24.32) MUTATED" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A1NK                      TCGA-EB-A24C 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A24D                      TCGA-EB-A3HV 
  "DEL PEAK 13(12Q24.32) MUTATED"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A3XB                      TCGA-EB-A3XC 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A3XF                      TCGA-EB-A3Y6 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-EB-A41A                      TCGA-EB-A41B 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-EB-A42Y                      TCGA-EB-A42Z 
"DEL PEAK 13(12Q24.32) WILD-TYPE"   "DEL PEAK 13(12Q24.32) MUTATED" 
                     TCGA-FR-A2OS                      TCGA-FR-A3R1 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-FS-A1ZN                      TCGA-GF-A2C7 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A263                      TCGA-GN-A269 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
                     TCGA-GN-A26C                      TCGA-IH-A3EA 
"DEL PEAK 13(12Q24.32) WILD-TYPE" "DEL PEAK 13(12Q24.32) WILD-TYPE" 
[1] "hr="     "8.1e+07"
D16V2, continuous
                                 vv
clus                              DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 13(12Q24.32) MUTATED                    1             7
  DEL PEAK 13(12Q24.32) WILD-TYPE                  1            18
                                 vv
clus                              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 13(12Q24.32) MUTATED                                                                                          1
  DEL PEAK 13(12Q24.32) WILD-TYPE                                                                                        1
D16V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 13(12Q24.32) MUTATED
  DISTANT METASTASIS                                                                                                   1
  PRIMARY TUMOR                                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                             1
                                                                                          clus
vv                                                                                         DEL PEAK 13(12Q24.32) WILD-TYPE
  DISTANT METASTASIS                                                                                                     1
  PRIMARY TUMOR                                                                                                         18
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                               1
D16V4, binary
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 13(12Q24.32) MUTATED      3    6
  DEL PEAK 13(12Q24.32) WILD-TYPE    6   14
        clus
vv       DEL PEAK 13(12Q24.32) MUTATED DEL PEAK 13(12Q24.32) WILD-TYPE
  FEMALE                             3                               6
  MALE                               6                              14
                                 vv
clus                              N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 13(12Q24.32) MUTATED    4   0   1   1   2   0  0  1
  DEL PEAK 13(12Q24.32) WILD-TYPE 11   1   0   0   1   1  3  2
D16V5, multiclass
D16V6, continuous
                                 vv
clus                              STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 13(12Q24.32) MUTATED          0        0         1         4
  DEL PEAK 13(12Q24.32) WILD-TYPE        1        1         0        11
                                 vv
clus                              STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 13(12Q24.32) MUTATED            0          2          1        0
  DEL PEAK 13(12Q24.32) WILD-TYPE          1          1          3        1
D16V7, multiclass

Clustering(17) Variable = Del Peak 14(15q15.1) mutation analysis
D17V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(15Q15.1) MUTATED    6  0
  DEL PEAK 14(15Q15.1) WILD-TYPE 11  5
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             6                             16 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 14(15Q15.1) MUTATED`
TCGA-EB-A24D TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A42Y TCGA-EB-A42Z TCGA-IH-A3EA 
        1.35         0.30         0.13         0.20         0.39        17.23 

$`DEL PEAK 14(15Q15.1) WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB 
        7.79         3.88         0.53         0.43         1.28         1.18 
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN 
        0.53         0.26         0.10        12.10        10.09        24.00 
TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C 
        0.03        15.35         5.59        26.99 

  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                         17.23                          26.99 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                         0.345                          2.580 
[1] "0.1 - 17.2 (0.3)" "0.0 - 27.0 (2.6)"
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 14(15Q15.1) MUTATED" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
  "DEL PEAK 14(15Q15.1) MUTATED"   "DEL PEAK 14(15Q15.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 14(15Q15.1) WILD-TYPE" "DEL PEAK 14(15Q15.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 14(15Q15.1) WILD-TYPE"   "DEL PEAK 14(15Q15.1) MUTATED" 
[1] "hr="     "2.6e+08"
D17V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 14(15Q15.1) MUTATED                    1             6
  DEL PEAK 14(15Q15.1) WILD-TYPE                  1            19
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 14(15Q15.1) MUTATED                                                                                          0
  DEL PEAK 14(15Q15.1) WILD-TYPE                                                                                        2
D17V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 14(15Q15.1) MUTATED
  DISTANT METASTASIS                                                                                                  1
  PRIMARY TUMOR                                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            0
                                                                                          clus
vv                                                                                         DEL PEAK 14(15Q15.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    1
  PRIMARY TUMOR                                                                                                        19
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
D17V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      2    5
  DEL PEAK 14(15Q15.1) WILD-TYPE    7   15
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  FEMALE                            2                              7
  MALE                              5                             15
                                vv
clus                             N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 14(15Q15.1) MUTATED    4   0   1   1   1   0  0  0
  DEL PEAK 14(15Q15.1) WILD-TYPE 11   1   0   0   2   1  3  3
D17V5, multiclass
D17V6, continuous
                                vv
clus                             STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 14(15Q15.1) MUTATED          0        0         0         4
  DEL PEAK 14(15Q15.1) WILD-TYPE        1        1         1        11
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 14(15Q15.1) MUTATED            0          2          1        0
  DEL PEAK 14(15Q15.1) WILD-TYPE          1          1          3        1
D17V7, multiclass

Clustering(18) Variable = Del Peak 15(16q23.3) mutation analysis
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(16Q23.3) MUTATED    6  1
  DEL PEAK 15(16Q23.3) WILD-TYPE 11  4
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                             7                             15 
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                             1                              4 
$`DEL PEAK 15(16Q23.3) MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-EB-A41B TCGA-GF-A2C7 
        3.88         1.35         0.13         0.53         0.10         0.03 
TCGA-GN-A269 
        5.59 

$`DEL PEAK 15(16Q23.3) WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        7.79         0.53         0.43         1.28         1.18         0.30 
TCGA-EB-A41A TCGA-EB-A42Y TCGA-EB-A42Z TCGA-FR-A2OS TCGA-FR-A3R1 TCGA-FS-A1ZN 
        0.26         0.20         0.39        12.10        10.09        24.00 
TCGA-GN-A263 TCGA-GN-A26C TCGA-IH-A3EA 
       15.35        26.99        17.23 

  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                          0.03                           0.20 
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                          5.59                          26.99 
  DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE 
                          0.53                           1.28 
[1] "0.0 - 5.6 (0.5)"  "0.2 - 27.0 (1.3)"
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 15(16Q23.3) MUTATED" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 15(16Q23.3) MUTATED"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 15(16Q23.3) MUTATED" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 15(16Q23.3) MUTATED"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
  "DEL PEAK 15(16Q23.3) MUTATED" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
  "DEL PEAK 15(16Q23.3) MUTATED"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 15(16Q23.3) WILD-TYPE"   "DEL PEAK 15(16Q23.3) MUTATED" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 15(16Q23.3) WILD-TYPE" "DEL PEAK 15(16Q23.3) WILD-TYPE" 
[1] "hr="     "3.6e+09"
D18V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 15(16Q23.3) MUTATED                    0             7
  DEL PEAK 15(16Q23.3) WILD-TYPE                  2            18
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 15(16Q23.3) MUTATED                                                                                          1
  DEL PEAK 15(16Q23.3) WILD-TYPE                                                                                        1
D18V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 15(16Q23.3) MUTATED
  DISTANT METASTASIS                                                                                                  0
  PRIMARY TUMOR                                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            1
                                                                                          clus
vv                                                                                         DEL PEAK 15(16Q23.3) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  PRIMARY TUMOR                                                                                                        18
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              1
D18V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(16Q23.3) MUTATED      2    6
  DEL PEAK 15(16Q23.3) WILD-TYPE    7   14
        clus
vv       DEL PEAK 15(16Q23.3) MUTATED DEL PEAK 15(16Q23.3) WILD-TYPE
  FEMALE                            2                              7
  MALE                              6                             14
                                vv
clus                             N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 15(16Q23.3) MUTATED    5   0   0   0   1   0  2  0
  DEL PEAK 15(16Q23.3) WILD-TYPE 10   1   1   1   2   1  1  3
D18V5, multiclass
D18V6, continuous
                                vv
clus                             STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 15(16Q23.3) MUTATED          0        0         0         5
  DEL PEAK 15(16Q23.3) WILD-TYPE        1        1         1        10
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 15(16Q23.3) MUTATED            0          1          2        0
  DEL PEAK 15(16Q23.3) WILD-TYPE          1          2          2        1
D18V7, multiclass

Clustering(19) Variable = Del Peak 16(22q12.1) mutation analysis
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(22Q12.1) MUTATED    4  0
  DEL PEAK 16(22Q12.1) WILD-TYPE 13  5
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                             4                             18 
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 16(22Q12.1) MUTATED`
TCGA-EB-A3Y6 TCGA-EB-A41A TCGA-EB-A41B TCGA-EB-A42Z 
        0.53         0.26         0.10         0.39 

$`DEL PEAK 16(22Q12.1) WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A42Y TCGA-FR-A2OS TCGA-FR-A3R1 
        1.18         0.30         0.13         0.20        12.10        10.09 
TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
       24.00         0.03        15.35         5.59        26.99        17.23 

  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                          0.10                           0.03 
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                          0.53                          26.99 
  DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE 
                         0.325                          2.615 
[1] "0.1 - 0.5 (0.3)"  "0.0 - 27.0 (2.6)"
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
  "DEL PEAK 16(22Q12.1) MUTATED"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
  "DEL PEAK 16(22Q12.1) MUTATED"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-D9-A1X3                     TCGA-D9-A3Z4 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A1NK                     TCGA-EB-A24C 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A24D                     TCGA-EB-A3HV 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XB                     TCGA-EB-A3XC 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-EB-A3XF                     TCGA-EB-A3Y6 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A41A                     TCGA-EB-A41B 
  "DEL PEAK 16(22Q12.1) MUTATED"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-EB-A42Y                     TCGA-EB-A42Z 
"DEL PEAK 16(22Q12.1) WILD-TYPE"   "DEL PEAK 16(22Q12.1) MUTATED" 
                    TCGA-FR-A2OS                     TCGA-FR-A3R1 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-FS-A1ZN                     TCGA-GF-A2C7 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A263                     TCGA-GN-A269 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
                    TCGA-GN-A26C                     TCGA-IH-A3EA 
"DEL PEAK 16(22Q12.1) WILD-TYPE" "DEL PEAK 16(22Q12.1) WILD-TYPE" 
[1] "hr=" NA   
D19V2, continuous
                                vv
clus                             DISTANT METASTASIS PRIMARY TUMOR
  DEL PEAK 16(22Q12.1) MUTATED                    0             4
  DEL PEAK 16(22Q12.1) WILD-TYPE                  2            21
                                vv
clus                             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  DEL PEAK 16(22Q12.1) MUTATED                                                                                          0
  DEL PEAK 16(22Q12.1) WILD-TYPE                                                                                        2
D19V3, multiclass
                                                                                          clus
vv                                                                                         DEL PEAK 16(22Q12.1) MUTATED
  DISTANT METASTASIS                                                                                                  0
  PRIMARY TUMOR                                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                            0
                                                                                          clus
vv                                                                                         DEL PEAK 16(22Q12.1) WILD-TYPE
  DISTANT METASTASIS                                                                                                    2
  PRIMARY TUMOR                                                                                                        21
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                              2
D19V4, binary
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(22Q12.1) MUTATED      2    2
  DEL PEAK 16(22Q12.1) WILD-TYPE    7   18
        clus
vv       DEL PEAK 16(22Q12.1) MUTATED DEL PEAK 16(22Q12.1) WILD-TYPE
  FEMALE                            2                              7
  MALE                              2                             18
                                vv
clus                             N0 N1A N1B N2A N2B N2C N3 NX
  DEL PEAK 16(22Q12.1) MUTATED    3   0   1   0   0   0  0  0
  DEL PEAK 16(22Q12.1) WILD-TYPE 12   1   0   1   3   1  3  3
D19V5, multiclass
D19V6, continuous
                                vv
clus                             STAGE IB STAGE II STAGE IIA STAGE IIC
  DEL PEAK 16(22Q12.1) MUTATED          0        0         0         3
  DEL PEAK 16(22Q12.1) WILD-TYPE        1        1         1        12
                                vv
clus                             STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEL PEAK 16(22Q12.1) MUTATED            0          0          1        0
  DEL PEAK 16(22Q12.1) WILD-TYPE          1          3          3        1
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")
