
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/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/SKCM-WT/3164458/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-WT/3215660/SKCM-WT.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-WT", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=SKCM-WT"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=23, in cluster file=35, common to both=23
[1] "Reduce the number of clustering variables from 80 to 40."
[1] 40 23
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                19 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                19 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                15 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                15 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                20 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                19 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                19 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                16 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                7                16 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                20 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                15 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                15 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                16 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                17 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                17 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                17 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                14 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                14 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 19 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 19 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 20 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 20 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 20 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 20 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 17 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 17 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 19 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 19 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 14 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 9                 14 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                10                 13 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 20 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 20 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 17 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 17 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                20 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                20 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                20 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                20 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                19 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                19 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                20 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                17 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                17 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                14 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                14 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                17 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 12 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 12 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 14 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 14 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 17 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 17 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 15 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 15 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 20 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 20 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                 19 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 18 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                 18 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 19 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 19 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 20 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 20 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 20 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 20 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 20 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 20 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 23 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-DA-A3F2 
          NA         1390           NA           NA           NA          589 
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
        2386          200           NA           NA           NA           NA 
TCGA-FS-A1ZU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T1 T1A  T2 T2A T3A T3B  T4 T4A T4B  TX 
  2   1   2   1   3   2   1   2   5   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 23 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=6, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2               0 1
  1P GAIN MUTATED   1 2
  1P GAIN WILD-TYPE 4 7
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                11 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                 7 
$`1P GAIN MUTATED`
TCGA-EE-A29D TCGA-ER-A3ET TCGA-GN-A26A 
       11.15         6.58        12.16 

$`1P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       12.99        78.44        15.35        31.33        14.70 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             6.58              4.93 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            12.16             78.44 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            11.15             15.35 
[1] "6.6 - 12.2 (11.2)" "4.9 - 78.4 (15.3)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS
  1P GAIN MUTATED                    1
  1P GAIN WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          2
  1P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                     1
  1P GAIN WILD-TYPE                  13
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     13
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    1
  1P GAIN WILD-TYPE    9   10
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                 9
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  1P GAIN MUTATED    1  0   2   1   0  0
  1P GAIN WILD-TYPE 10  1   0   2   2  2
D1V5, multiclass
D1V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  1P GAIN MUTATED         0        0        0         0         1         0
  1P GAIN WILD-TYPE       4        1        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED            2          0          1
  1P GAIN WILD-TYPE          0          2          3
D1V7, multiclass

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

$`1Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-ER-A19L TCGA-ER-A1A1 
       10.26        45.70        24.00        19.36        12.99        78.44 
TCGA-GN-A261 TCGA-GN-A264 
       15.35        31.33 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             4.93             10.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            14.70             78.44 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            8.865            21.680 
[1] "4.9 - 14.7 (8.9)"   "10.3 - 78.4 (21.7)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "5.5"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS
  1Q GAIN MUTATED                    3
  1Q GAIN WILD-TYPE                  0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                          2
  1Q GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                     3
  1Q GAIN WILD-TYPE                  11
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      5    3
  1Q GAIN WILD-TYPE    7    8
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               5                 7
  MALE                 3                 8
                   vv
clus                N0 N1 N1A N1B N2B N3
  1Q GAIN MUTATED    4  0   2   2   0  0
  1Q GAIN WILD-TYPE  7  1   0   1   2  2
D2V5, multiclass
D2V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  1Q GAIN MUTATED         0        0        1         1         2         0
  1Q GAIN WILD-TYPE       4        1        0         1         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED            2          1          1
  1Q GAIN WILD-TYPE          0          1          3
D2V7, multiclass

Clustering(3) Variable = 3p gain mutation analysis
D3V1, survival
                   sevent
clus2               0 1
  3P GAIN MUTATED   1 1
  3P GAIN WILD-TYPE 4 8
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                12 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 8 
$`3P GAIN MUTATED`
TCGA-DA-A1IA TCGA-ER-A3ET 
        4.93         6.58 

$`3P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99        78.44        15.35        31.33        12.16        14.70 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             4.93              6.31 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6.58             78.44 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            5.755            15.025 
[1] "4.9 - 6.6 (5.8)"   "6.3 - 78.4 (15.0)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                12 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A3F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L        TCGA-ER-A1A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A264        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V2, continuous
                   vv
clus                DISTANT METASTASIS
  3P GAIN MUTATED                    2
  3P GAIN WILD-TYPE                  1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          1
  3P GAIN WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     0
  3P GAIN WILD-TYPE                  14
D3V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    0
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     14
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    1
  3P GAIN WILD-TYPE   10   10
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                10
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  3P GAIN MUTATED    1  0   1   1   0  0
  3P GAIN WILD-TYPE 10  1   1   2   2  2
D3V5, multiclass
D3V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  3P GAIN MUTATED         0        0        1         0         0         0
  3P GAIN WILD-TYPE       4        1        0         2         3         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED            1          1          0
  3P GAIN WILD-TYPE          1          1          4
D3V7, multiclass

Clustering(4) Variable = 3q gain mutation analysis
D4V1, survival
                   sevent
clus2               0 1
  3Q GAIN MUTATED   1 2
  3Q GAIN WILD-TYPE 4 7
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 7 
$`3Q GAIN MUTATED`
TCGA-DA-A1IA TCGA-ER-A3ET TCGA-GN-A26A 
        4.93         6.58        12.16 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       12.99        78.44        15.35        31.33        14.70 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             4.93              6.31 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.16             78.44 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             6.58             15.35 
[1] "4.9 - 12.2 (6.6)"  "6.3 - 78.4 (15.3)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
[1] "hr=" "4.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS
  3Q GAIN MUTATED                    2
  3Q GAIN WILD-TYPE                  1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          2
  3Q GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     0
  3Q GAIN WILD-TYPE                  14
D4V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    0
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     14
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3    1
  3Q GAIN WILD-TYPE    9   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                 9
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  3Q GAIN MUTATED    1  0   2   1   0  0
  3Q GAIN WILD-TYPE 10  1   0   2   2  2
D4V5, multiclass
D4V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  3Q GAIN MUTATED         0        0        1         0         0         0
  3Q GAIN WILD-TYPE       4        1        0         2         3         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED            2          1          0
  3Q GAIN WILD-TYPE          0          1          4
D4V7, multiclass

Clustering(5) Variable = 4p gain mutation analysis
D5V1, survival
                   sevent
clus2               0 1
  4P GAIN MUTATED   2 1
  4P GAIN WILD-TYPE 3 8
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 8 
$`4P GAIN MUTATED`
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26D 
        6.58        31.33        14.70 

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

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             6.58              4.93 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            31.33             78.44 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.70             12.99 
[1] "6.6 - 31.3 (14.7)" "4.9 - 78.4 (13.0)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr=" "2.4"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS
  4P GAIN MUTATED                    2
  4P GAIN WILD-TYPE                  1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          1
  4P GAIN WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                     4
  4P GAIN WILD-TYPE                  10
D5V3, multiclass
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     10
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    3
  4P GAIN WILD-TYPE    8    8
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4                 8
  MALE                 3                 8
                   vv
clus                N0 N1 N1A N1B N2B N3
  4P GAIN MUTATED    5  0   1   0   0  0
  4P GAIN WILD-TYPE  6  1   1   3   2  2
D5V5, multiclass
D5V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  4P GAIN MUTATED         1        1        1         0         2         0
  4P GAIN WILD-TYPE       3        0        0         2         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED            1          0          0
  4P GAIN WILD-TYPE          1          2          4
D5V7, multiclass

Clustering(6) Variable = 4q gain mutation analysis
D6V1, survival
                   sevent
clus2               0 1
  4Q GAIN MUTATED   1 1
  4Q GAIN WILD-TYPE 4 8
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                12 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                 8 
$`4Q GAIN MUTATED`
TCGA-GN-A264 TCGA-GN-A26D 
       31.33        14.70 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A 
       11.15        12.99        78.44         6.58        15.35        12.16 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            14.70              4.93 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            31.33             78.44 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           23.015            12.575 
[1] "14.7 - 31.3 (23.0)" "4.9 - 78.4 (12.6)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                12 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A26A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D6V2, continuous
                   vv
clus                DISTANT METASTASIS
  4Q GAIN MUTATED                    1
  4Q GAIN WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          0
  4Q GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                     2
  4Q GAIN WILD-TYPE                  12
D6V3, multiclass
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     12
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    1
  4Q GAIN WILD-TYPE   10   10
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                10
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  4Q GAIN MUTATED    2  0   0   0   0  0
  4Q GAIN WILD-TYPE  9  1   2   3   2  2
D6V5, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                19 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-D9-A149 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IA        TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2GI        TCGA-EE-A2GK        TCGA-EE-A2MR        TCGA-ER-A1A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-FS-A1Z4        TCGA-FS-A1ZG        TCGA-FS-A1ZJ 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZK        TCGA-GN-A261        TCGA-GN-A26A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D6V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  4Q GAIN MUTATED         0        0        0         0         2         0
  4Q GAIN WILD-TYPE       4        1        1         2         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED            0          0          0
  4Q GAIN WILD-TYPE          2          2          4
D6V7, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                18 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-EE-A2GI 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2GK        TCGA-EE-A2MR        TCGA-ER-A1A1        TCGA-ER-A3ET 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1ZG        TCGA-FS-A1ZJ        TCGA-FS-A1ZK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A26A 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(7) Variable = 6p gain mutation analysis
D7V1, survival
                   sevent
clus2               0 1
  6P GAIN MUTATED   1 4
  6P GAIN WILD-TYPE 4 5
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                 9 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                 5 
$`6P GAIN MUTATED`
TCGA-DA-A1IA TCGA-EE-A17Z TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        4.93         6.31        31.33        12.16        14.70 

$`6P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A19L 
       10.26        45.70        24.00        19.36        11.15        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       78.44         6.58        15.35 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.93              6.58 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            31.33             78.44 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            12.16             15.35 
[1] "4.9 - 31.3 (12.2)" "6.6 - 78.4 (15.3)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" 
[1] "hr=" "2"  
D7V2, continuous
                   vv
clus                DISTANT METASTASIS
  6P GAIN MUTATED                    3
  6P GAIN WILD-TYPE                  0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          2
  6P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                     3
  6P GAIN WILD-TYPE                  11
D7V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    3
  6P GAIN WILD-TYPE    7    8
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5                 7
  MALE                 3                 8
                   vv
clus                N0 N1 N1A N1B N2B N3
  6P GAIN MUTATED    4  0   1   2   0  0
  6P GAIN WILD-TYPE  7  1   1   1   2  2
D7V5, multiclass
D7V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  6P GAIN MUTATED         0        0        1         1         2         0
  6P GAIN WILD-TYPE       4        1        0         1         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED            1          1          0
  6P GAIN WILD-TYPE          1          1          4
D7V7, multiclass

Clustering(8) Variable = 7p gain mutation analysis
D8V1, survival
                   sevent
clus2               0 1
  7P GAIN MUTATED   1 4
  7P GAIN WILD-TYPE 4 5
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                 9 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                4                 5 
$`7P GAIN MUTATED`
TCGA-DA-A1IA TCGA-EE-A29D TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        4.93        11.15        31.33        12.16        14.70 

$`7P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        45.70        24.00        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       78.44         6.58        15.35 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.93              6.31 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            31.33             78.44 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            12.16             15.35 
[1] "4.9 - 31.3 (12.2)" "6.3 - 78.4 (15.3)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "1.8"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS
  7P GAIN MUTATED                    1
  7P GAIN WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                          2
  7P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                     4
  7P GAIN WILD-TYPE                  10
D8V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     10
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    3
  7P GAIN WILD-TYPE    8    8
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               4                 8
  MALE                 3                 8
                   vv
clus                N0 N1 N1A N1B N2B N3
  7P GAIN MUTATED    2  0   1   3   0  0
  7P GAIN WILD-TYPE  9  1   1   0   2  2
D8V5, multiclass
D8V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  7P GAIN MUTATED         0        1        0         0         1         0
  7P GAIN WILD-TYPE       4        0        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED            1          1          1
  7P GAIN WILD-TYPE          1          1          3
D8V7, multiclass

Clustering(9) Variable = 7q gain mutation analysis
D9V1, survival
                   sevent
clus2               0 1
  7Q GAIN MUTATED   1 3
  7Q GAIN WILD-TYPE 4 6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 6 
$`7Q GAIN MUTATED`
TCGA-DA-A1IA TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        4.93        31.33        12.16        14.70 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       12.99        78.44         6.58        15.35 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.93              6.31 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            31.33             78.44 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.43             14.17 
[1] "4.9 - 31.3 (13.4)" "6.3 - 78.4 (14.2)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS
  7Q GAIN MUTATED                    1
  7Q GAIN WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                          2
  7Q GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                     3
  7Q GAIN WILD-TYPE                  11
D9V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    2
  7Q GAIN WILD-TYPE    8    9
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               4                 8
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  7Q GAIN MUTATED    2  0   1   2   0  0
  7Q GAIN WILD-TYPE  9  1   1   1   2  2
D9V5, multiclass
D9V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  7Q GAIN MUTATED         0        1        0         0         1         0
  7Q GAIN WILD-TYPE       4        0        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED            1          1          0
  7Q GAIN WILD-TYPE          1          1          4
D9V7, multiclass

Clustering(10) Variable = 8p gain mutation analysis
D10V1, survival
                   sevent
clus2               0 1
  8P GAIN MUTATED   3 2
  8P GAIN WILD-TYPE 2 7
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                 9 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 7 
$`8P GAIN MUTATED`
TCGA-D3-A3CC TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A26A TCGA-GN-A26D 
       45.70        12.99         6.58        12.16        14.70 

$`8P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A1A1 TCGA-GN-A261 TCGA-GN-A264 
       78.44        15.35        31.33 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             6.58              4.93 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            45.70             78.44 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            12.99             15.35 
[1] "6.6 - 45.7 (13.0)" "4.9 - 78.4 (15.3)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" 
[1] "hr=" "1.8"
D10V2, continuous
                   vv
clus                DISTANT METASTASIS
  8P GAIN MUTATED                    1
  8P GAIN WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                          3
  8P GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                     2
  8P GAIN WILD-TYPE                  12
D10V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     12
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    2
  8P GAIN WILD-TYPE    8    9
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               4                 8
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  8P GAIN MUTATED    3  0   2   0   0  0
  8P GAIN WILD-TYPE  8  1   0   3   2  2
D10V5, multiclass
D10V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  8P GAIN MUTATED         0        0        1         0         2         0
  8P GAIN WILD-TYPE       4        1        0         2         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED            2          0          0
  8P GAIN WILD-TYPE          0          2          4
D10V7, multiclass

Clustering(11) Variable = 8q gain mutation analysis
D11V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   3 4
  8Q GAIN WILD-TYPE 2 5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                 7 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                 5 
$`8Q GAIN MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A26A 
       10.26        45.70         6.31        12.99         6.58        12.16 
TCGA-GN-A26D 
       14.70 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A1A1 TCGA-GN-A261 
       24.00         4.93        19.36        11.15        78.44        15.35 
TCGA-GN-A264 
       31.33 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.31              4.93 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            45.70             78.44 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.16             19.36 
[1] "6.3 - 45.7 (12.2)" "4.9 - 78.4 (19.4)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS
  8Q GAIN MUTATED                    2
  8Q GAIN WILD-TYPE                  1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                          3
  8Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                     4
  8Q GAIN WILD-TYPE                  10
D11V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     10
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    4
  8Q GAIN WILD-TYPE    7    7
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                 7
  MALE                 4                 7
                   vv
clus                N0 N1 N1A N1B N2B N3
  8Q GAIN MUTATED    6  0   2   0   0  0
  8Q GAIN WILD-TYPE  5  1   0   3   2  2
D11V5, multiclass
D11V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  8Q GAIN MUTATED         0        0        1         2         3         0
  8Q GAIN WILD-TYPE       4        1        0         0         0         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED            2          0          0
  8Q GAIN WILD-TYPE          0          2          4
D11V7, multiclass

Clustering(12) Variable = 12p gain mutation analysis
D12V1, survival
                    sevent
clus2                0 1
  12P GAIN MUTATED   0 3
  12P GAIN WILD-TYPE 5 6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 11 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  6 
$`12P GAIN MUTATED`
TCGA-DA-A1IA TCGA-ER-A19L TCGA-GN-A26A 
        4.93        12.99        12.16 

$`12P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       78.44         6.58        15.35        31.33        14.70 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.93               6.31 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.99              78.44 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.16              15.35 
[1] "4.9 - 13.0 (12.2)" "6.3 - 78.4 (15.3)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
[1] "hr=" "4.5"
D12V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12P GAIN MUTATED                    2
  12P GAIN WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          1
  12P GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                     1
  12P GAIN WILD-TYPE                  13
D12V3, multiclass
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      13
D12V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    1
  12P GAIN WILD-TYPE    9   10
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                  9
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  12P GAIN MUTATED    1  0   1   1   0  0
  12P GAIN WILD-TYPE 10  1   1   2   2  2
D12V5, multiclass
D12V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  12P GAIN MUTATED         0        0        0         0         1         0
  12P GAIN WILD-TYPE       4        1        1         2         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  12P GAIN MUTATED            1          1          0
  12P GAIN WILD-TYPE          1          1          4
D12V7, multiclass

Clustering(13) Variable = 12q gain mutation analysis
D13V1, survival
                    sevent
clus2                0 1
  12Q GAIN MUTATED   0 2
  12Q GAIN WILD-TYPE 5 7
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 12 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                  7 
$`12Q GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A26A 
       12.99        12.16 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       11.15        78.44         6.58        15.35        31.33        14.70 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.16               4.93 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             12.99              78.44 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            12.575             15.025 
[1] "12.2 - 13.0 (12.6)" "4.9 - 78.4 (15.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D13V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12Q GAIN MUTATED                    1
  12Q GAIN WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q GAIN MUTATED                                                                                          1
  12Q GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                     1
  12Q GAIN WILD-TYPE                  13
D13V3, multiclass
                                                                                          clus
vv                                                                                         12Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      13
D13V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    2
  12Q GAIN WILD-TYPE   11    9
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 11
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  12Q GAIN MUTATED    1  0   1   0   0  0
  12Q GAIN WILD-TYPE 10  1   1   3   2  2
D13V5, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 19 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A149         TCGA-DA-A1IA         TCGA-DA-A3F2 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A29D         TCGA-EE-A2GI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2MR         TCGA-ER-A1A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FS-A1Z4         TCGA-FS-A1ZG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZJ         TCGA-FS-A1ZU         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" 
D13V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  12Q GAIN MUTATED         0        0        1         0         0         0
  12Q GAIN WILD-TYPE       4        1        0         2         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN MUTATED            1          0          0
  12Q GAIN WILD-TYPE          1          2          4
D13V7, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 18 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A2GI         TCGA-EE-A2GK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2MR         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z4         TCGA-FS-A1ZG         TCGA-FS-A1ZJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-GN-A261         TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 

Clustering(14) Variable = 15q gain mutation analysis
D14V1, survival
                    sevent
clus2                0 1
  15Q GAIN MUTATED   0 2
  15Q GAIN WILD-TYPE 5 7
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 12 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                  7 
$`15Q GAIN MUTATED`
TCGA-EE-A29D TCGA-GN-A264 
       11.15        31.33 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A TCGA-GN-A26D 
       12.99        78.44         6.58        15.35        12.16        14.70 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             11.15               4.93 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             31.33              78.44 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            21.240             13.845 
[1] "11.2 - 31.3 (21.2)" "4.9 - 78.4 (13.8)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D14V2, continuous
                    vv
clus                 DISTANT METASTASIS
  15Q GAIN MUTATED                    0
  15Q GAIN WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          1
  15Q GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                     2
  15Q GAIN WILD-TYPE                  12
D14V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      12
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1    2
  15Q GAIN WILD-TYPE   11    9
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                1                 11
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  15Q GAIN MUTATED    0  0   0   2   0  0
  15Q GAIN WILD-TYPE 11  1   2   1   2  2
D14V5, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 19 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GI         TCGA-EE-A2GK         TCGA-EE-A2MR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FS-A1Z4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZJ         TCGA-FS-A1ZK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-GN-A261         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" 
D14V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  15Q GAIN MUTATED         0        0        0         0         0         0
  15Q GAIN WILD-TYPE       4        1        1         2         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  15Q GAIN MUTATED            0          0          1
  15Q GAIN WILD-TYPE          2          2          3
D14V7, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 19 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2GI         TCGA-EE-A2GK         TCGA-EE-A2MR 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FS-A1Z4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZJ         TCGA-FS-A1ZK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-GN-A261         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" 

Clustering(15) Variable = 17q gain mutation analysis
D15V1, survival
                    sevent
clus2                0 1
  17Q GAIN MUTATED   1 1
  17Q GAIN WILD-TYPE 4 8
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 12 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                  8 
$`17Q GAIN MUTATED`
TCGA-DA-A1IA TCGA-GN-A26D 
        4.93        14.70 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       12.99        78.44         6.58        15.35        31.33        12.16 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              4.93               6.31 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.70              78.44 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             9.815             14.170 
[1] "4.9 - 14.7 (9.8)"  "6.3 - 78.4 (14.2)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-EE-A17Z         TCGA-EE-A29D 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26A 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
D15V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17Q GAIN MUTATED                    2
  17Q GAIN WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          0
  17Q GAIN WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                     1
  17Q GAIN WILD-TYPE                  13
D15V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      13
D15V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    0
  17Q GAIN WILD-TYPE    9   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                  9
  MALE                  0                 11
                    vv
clus                 N0 N1 N1A N1B N2B N3
  17Q GAIN MUTATED    2  0   0   1   0  0
  17Q GAIN WILD-TYPE  9  1   2   2   2  2
D15V5, multiclass
D15V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  17Q GAIN MUTATED         0        0        0         0         2         0
  17Q GAIN WILD-TYPE       4        1        1         2         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED            0          1          0
  17Q GAIN WILD-TYPE          2          1          4
D15V7, multiclass

Clustering(16) Variable = 18p gain mutation analysis
D16V1, survival
                    sevent
clus2                0 1
  18P GAIN MUTATED   2 1
  18P GAIN WILD-TYPE 3 8
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 11 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                  8 
$`18P GAIN MUTATED`
TCGA-D3-A3CC TCGA-GN-A26A TCGA-GN-A26D 
       45.70        12.16        14.70 

$`18P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 
       12.99        78.44         6.58        15.35        31.33 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             12.16               4.93 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             45.70              78.44 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.70              12.99 
[1] "12.2 - 45.7 (14.7)" "4.9 - 78.4 (13.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
[1] "hr=" "2.9"
D16V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18P GAIN MUTATED                    2
  18P GAIN WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          2
  18P GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                     2
  18P GAIN WILD-TYPE                  12
D16V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      12
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    1
  18P GAIN WILD-TYPE    7   10
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                5                  7
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  18P GAIN MUTATED    5  0   1   0   0  0
  18P GAIN WILD-TYPE  6  1   1   3   2  2
D16V5, multiclass
D16V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  18P GAIN MUTATED         1        0        1         0         3         0
  18P GAIN WILD-TYPE       3        1        0         2         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  18P GAIN MUTATED            1          0          0
  18P GAIN WILD-TYPE          1          2          4
D16V7, multiclass

Clustering(17) Variable = 18q gain mutation analysis
D17V1, survival
                    sevent
clus2                0 1
  18Q GAIN MUTATED   2 1
  18Q GAIN WILD-TYPE 3 8
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 11 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                  8 
$`18Q GAIN MUTATED`
TCGA-D3-A3CC TCGA-GN-A26A TCGA-GN-A26D 
       45.70        12.16        14.70 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 
       12.99        78.44         6.58        15.35        31.33 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             12.16               4.93 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             45.70              78.44 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.70              12.99 
[1] "12.2 - 45.7 (14.7)" "4.9 - 78.4 (13.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
[1] "hr=" "2.9"
D17V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18Q GAIN MUTATED                    1
  18Q GAIN WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          2
  18Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     1
  18Q GAIN WILD-TYPE                  13
D17V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      13
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    0
  18Q GAIN WILD-TYPE    8   11
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                  8
  MALE                  0                 11
                    vv
clus                 N0 N1 N1A N1B N2B N3
  18Q GAIN MUTATED    3  0   1   0   0  0
  18Q GAIN WILD-TYPE  8  1   1   3   2  2
D17V5, multiclass
D17V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  18Q GAIN MUTATED         0        0        0         0         3         0
  18Q GAIN WILD-TYPE       4        1        1         2         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  18Q GAIN MUTATED            1          0          0
  18Q GAIN WILD-TYPE          1          2          4
D17V7, multiclass

Clustering(18) Variable = 20p gain mutation analysis
D18V1, survival
                    sevent
clus2                0 1
  20P GAIN MUTATED   1 3
  20P GAIN WILD-TYPE 4 6
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                 10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  6 
$`20P GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99        31.33        12.16        14.70 

$`20P GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       11.15        78.44         6.58        15.35 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             12.16               4.93 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             31.33              78.44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.845             13.250 
[1] "12.2 - 31.3 (13.8)" "4.9 - 78.4 (13.2)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
[1] "hr=" "1"  
D18V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20P GAIN MUTATED                    2
  20P GAIN WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                          1
  20P GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                     6
  20P GAIN WILD-TYPE                   8
D18V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    4
  20P GAIN WILD-TYPE    7    7
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                  7
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  20P GAIN MUTATED    5  0   1   0   1  0
  20P GAIN WILD-TYPE  6  1   1   3   1  2
D18V5, multiclass
D18V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  20P GAIN MUTATED         1        1        1         0         2         0
  20P GAIN WILD-TYPE       3        0        0         2         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED            1          0          1
  20P GAIN WILD-TYPE          1          2          3
D18V7, multiclass

Clustering(19) Variable = 20q gain mutation analysis
D19V1, survival
                    sevent
clus2                0 1
  20Q GAIN MUTATED   1 4
  20Q GAIN WILD-TYPE 4 5
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                  9 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                  5 
$`20Q GAIN MUTATED`
TCGA-DA-A1IA TCGA-ER-A19L TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        4.93        12.99        31.33        12.16        14.70 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       78.44         6.58        15.35 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              4.93               6.31 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             31.33              78.44 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.99              15.35 
[1] "4.9 - 31.3 (13.0)" "6.3 - 78.4 (15.3)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
[1] "hr=" "1.6"
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20Q GAIN MUTATED                    3
  20Q GAIN WILD-TYPE                  0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                          1
  20Q GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                     6
  20Q GAIN WILD-TYPE                   8
D19V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    4
  20Q GAIN WILD-TYPE    6    7
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                  6
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  20Q GAIN MUTATED    5  0   1   1   1  0
  20Q GAIN WILD-TYPE  6  1   1   2   1  2
D19V5, multiclass
D19V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  20Q GAIN MUTATED         1        1        1         0         2         0
  20Q GAIN WILD-TYPE       3        0        0         2         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED            1          1          1
  20Q GAIN WILD-TYPE          1          1          3
D19V7, multiclass

Clustering(20) Variable = 21q gain mutation analysis
D20V1, survival
                    sevent
clus2                0 1
  21Q GAIN MUTATED   1 1
  21Q GAIN WILD-TYPE 4 8
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 12 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                  8 
$`21Q GAIN MUTATED`
TCGA-ER-A19L TCGA-GN-A26D 
       12.99        14.70 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       11.15        78.44         6.58        15.35        31.33        12.16 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             12.99               4.93 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.70              78.44 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            13.845             13.755 
[1] "13.0 - 14.7 (13.8)" "4.9 - 78.4 (13.8)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS
  21Q GAIN MUTATED                    0
  21Q GAIN WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          0
  21Q GAIN WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                     3
  21Q GAIN WILD-TYPE                  11
D20V3, multiclass
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      11
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   10   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 10
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  21Q GAIN MUTATED    2  0   0   0   0  0
  21Q GAIN WILD-TYPE  9  1   2   3   2  2
D20V5, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 19 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A149         TCGA-DA-A1IA         TCGA-DA-A3F2 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A17Z         TCGA-EE-A29D         TCGA-EE-A2GI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2MR         TCGA-ER-A1A1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FS-A1Z4         TCGA-FS-A1ZG 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZK         TCGA-FS-A1ZU         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" 
D20V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  21Q GAIN MUTATED         1        0        0         0         1         0
  21Q GAIN WILD-TYPE       3        1        1         2         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED            0          0          0
  21Q GAIN WILD-TYPE          2          2          4
D20V7, multiclass
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 18 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A2GI         TCGA-EE-A2GK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2MR         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1Z4         TCGA-FS-A1ZG         TCGA-FS-A1ZK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-GN-A261         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 

Clustering(21) Variable = 22q gain mutation analysis
D21V1, survival
                    sevent
clus2                0 1
  22Q GAIN MUTATED   2 3
  22Q GAIN WILD-TYPE 3 6
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                  9 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                  6 
$`22Q GAIN MUTATED`
TCGA-DA-A1IA TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        4.93         6.58        31.33        12.16        14.70 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70        24.00        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-GN-A261 
       12.99        78.44        15.35 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              4.93               6.31 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             31.33              78.44 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             12.16              15.35 
[1] "4.9 - 31.3 (12.2)" "6.3 - 78.4 (15.3)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
[1] "hr=" "1.3"
D21V2, continuous
                    vv
clus                 DISTANT METASTASIS
  22Q GAIN MUTATED                    2
  22Q GAIN WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                          2
  22Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                     2
  22Q GAIN WILD-TYPE                  12
D21V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      12
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    1
  22Q GAIN WILD-TYPE    7   10
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                  7
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  22Q GAIN MUTATED    2  0   2   1   0  0
  22Q GAIN WILD-TYPE  9  1   0   2   2  2
D21V5, multiclass
D21V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  22Q GAIN MUTATED         0        0        0         0         2         0
  22Q GAIN WILD-TYPE       4        1        1         2         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED            2          1          0
  22Q GAIN WILD-TYPE          0          1          4
D21V7, multiclass

Clustering(22) Variable = 1p loss mutation analysis
D22V1, survival
                   sevent
clus2               0 1
  1P LOSS MUTATED   2 1
  1P LOSS WILD-TYPE 3 8
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                11 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 8 
$`1P LOSS MUTATED`
TCGA-D3-A3CC TCGA-ER-A19L TCGA-GN-A26D 
       45.70        12.99        14.70 

$`1P LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       78.44         6.58        15.35        31.33        12.16 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            12.99              4.93 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            45.70             78.44 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            14.70             12.16 
[1] "13.0 - 45.7 (14.7)" "4.9 - 78.4 (12.2)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "3.1"
D22V2, continuous
                   vv
clus                DISTANT METASTASIS
  1P LOSS MUTATED                    0
  1P LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          1
  1P LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     2
  1P LOSS WILD-TYPE                  12
D22V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     12
D22V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    1
  1P LOSS WILD-TYPE   10   10
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                10
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  1P LOSS MUTATED    2  0   0   0   0  0
  1P LOSS WILD-TYPE  9  1   2   3   2  2
D22V5, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                19 
       TCGA-D3-A2J6        TCGA-D3-A3CF        TCGA-D9-A149        TCGA-DA-A1IA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-EE-A2GI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2GK        TCGA-EE-A2MR        TCGA-ER-A1A1        TCGA-ER-A3ET 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1ZG        TCGA-FS-A1ZJ        TCGA-FS-A1ZK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZU        TCGA-GN-A261        TCGA-GN-A26A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D22V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  1P LOSS MUTATED         0        0        0         0         2         0
  1P LOSS WILD-TYPE       4        1        1         2         1         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED            0          0          0
  1P LOSS WILD-TYPE          2          2          4
D22V7, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                18 
       TCGA-D3-A2J6        TCGA-D3-A3CF        TCGA-DA-A1IA        TCGA-DA-A3F2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-EE-A2GI        TCGA-EE-A2GK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FS-A1Z4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZG        TCGA-FS-A1ZJ        TCGA-FS-A1ZK        TCGA-FS-A1ZU 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A26A 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 

Clustering(23) Variable = 2p loss mutation analysis
D23V1, survival
                   sevent
clus2               0 1
  2P LOSS MUTATED   1 2
  2P LOSS WILD-TYPE 4 7
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                11 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                 7 
$`2P LOSS MUTATED`
TCGA-D3-A3CF TCGA-GN-A264 TCGA-GN-A26D 
       24.00        31.33        14.70 

$`2P LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       10.26        45.70         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A 
       12.99        78.44         6.58        15.35        12.16 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            14.70              4.93 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            31.33             78.44 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            24.00             12.16 
[1] "14.7 - 31.3 (24.0)" "4.9 - 78.4 (12.2)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "hr=" "1.7"
D23V2, continuous
                   vv
clus                DISTANT METASTASIS
  2P LOSS MUTATED                    0
  2P LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P LOSS MUTATED                                                                                          0
  2P LOSS WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                     3
  2P LOSS WILD-TYPE                  11
D23V3, multiclass
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     11
D23V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE   10   10
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                10
  MALE                 1                10
                   vv
clus                N0 N1 N1A N1B N2B N3
  2P LOSS MUTATED    1  0   0   0   0  1
  2P LOSS WILD-TYPE 10  1   2   3   2  1
D23V5, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                19 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D9-A149        TCGA-DA-A1IA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-EE-A2GI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2GK        TCGA-EE-A2MR        TCGA-ER-A1A1        TCGA-ER-A3ET 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1ZG        TCGA-FS-A1ZJ        TCGA-FS-A1ZK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZU        TCGA-GN-A261        TCGA-GN-A26A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D23V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  2P LOSS MUTATED         0        0        0         0         1         0
  2P LOSS WILD-TYPE       4        1        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED            0          0          1
  2P LOSS WILD-TYPE          2          2          3
D23V7, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                18 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-DA-A1IA        TCGA-DA-A3F2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-EE-A2GI        TCGA-EE-A2GK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-FS-A1Z4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A1ZG        TCGA-FS-A1ZJ        TCGA-FS-A1ZK        TCGA-FS-A1ZU 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A26A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 

Clustering(24) Variable = 2q loss mutation analysis
D24V1, survival
                   sevent
clus2               0 1
  2Q LOSS MUTATED   1 3
  2Q LOSS WILD-TYPE 4 6
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                10 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                 6 
$`2Q LOSS MUTATED`
TCGA-D3-A3CF TCGA-EE-A29D TCGA-GN-A264 TCGA-GN-A26D 
       24.00        11.15        31.33        14.70 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        45.70         4.93        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26A 
       78.44         6.58        15.35        12.16 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            11.15              4.93 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            31.33             78.44 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           19.350            12.575 
[1] "11.2 - 31.3 (19.4)" "4.9 - 78.4 (12.6)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "hr=" "1.1"
D24V2, continuous
                   vv
clus                DISTANT METASTASIS
  2Q LOSS MUTATED                    0
  2Q LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q LOSS MUTATED                                                                                          0
  2Q LOSS WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                     4
  2Q LOSS WILD-TYPE                  10
D24V3, multiclass
                                                                                          clus
vv                                                                                         2Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     10
D24V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   10    9
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                10
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  2Q LOSS MUTATED    1  0   0   1   0  1
  2Q LOSS WILD-TYPE 10  1   2   2   2  1
D24V5, multiclass
D24V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  2Q LOSS MUTATED         0        0        0         0         1         0
  2Q LOSS WILD-TYPE       4        1        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED            0          0          2
  2Q LOSS WILD-TYPE          2          2          2
D24V7, multiclass

Clustering(25) Variable = 4p loss mutation analysis
D25V1, survival
                   sevent
clus2               0 1
  4P LOSS MUTATED   1 2
  4P LOSS WILD-TYPE 4 7
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                11 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 7 
$`4P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-EE-A29D 
       10.26        45.70        11.15 

$`4P LOSS WILD-TYPE`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A1A1 
       24.00         4.93        19.36         6.31        12.99        78.44 
TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        6.58        15.35        31.33        12.16        14.70 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            10.26              4.93 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            45.70             78.44 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            11.15             14.70 
[1] "10.3 - 45.7 (11.2)" "4.9 - 78.4 (14.7)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D25V2, continuous
                   vv
clus                DISTANT METASTASIS
  4P LOSS MUTATED                    0
  4P LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          1
  4P LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     2
  4P LOSS WILD-TYPE                  12
D25V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     12
D25V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    2
  4P LOSS WILD-TYPE   11    9
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               1                11
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  4P LOSS MUTATED    2  0   0   1   0  0
  4P LOSS WILD-TYPE  9  1   2   2   2  2
D25V5, multiclass
D25V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  4P LOSS MUTATED         0        0        0         1         1         0
  4P LOSS WILD-TYPE       4        1        1         1         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED            0          0          1
  4P LOSS WILD-TYPE          2          2          3
D25V7, multiclass

Clustering(26) Variable = 6q loss mutation analysis
D26V1, survival
                   sevent
clus2               0 1
  6Q LOSS MUTATED   0 3
  6Q LOSS WILD-TYPE 5 6
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                 6 
$`6Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29D TCGA-GN-A26A 
       10.26        11.15        12.16 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       45.70        24.00         4.93        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       78.44         6.58        15.35        31.33        14.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            10.26              4.93 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.16             78.44 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            11.15             15.35 
[1] "10.3 - 12.2 (11.2)" "4.9 - 78.4 (15.3)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "6.1"
D26V2, continuous
                   vv
clus                DISTANT METASTASIS
  6Q LOSS MUTATED                    1
  6Q LOSS WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                          1
  6Q LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                     4
  6Q LOSS WILD-TYPE                  10
D26V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     10
D26V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    2
  6Q LOSS WILD-TYPE    8    9
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                 8
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  6Q LOSS MUTATED    3  0   1   1   1  0
  6Q LOSS WILD-TYPE  8  1   1   2   1  2
D26V5, multiclass
D26V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  6Q LOSS MUTATED         1        0        0         1         1         0
  6Q LOSS WILD-TYPE       3        1        1         1         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED            1          0          2
  6Q LOSS WILD-TYPE          1          2          2
D26V7, multiclass

Clustering(27) Variable = 9p loss mutation analysis
D27V1, survival
                   sevent
clus2               0 1
  9P LOSS MUTATED   1 6
  9P LOSS WILD-TYPE 4 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                 7 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                6                 3 
$`9P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A29D TCGA-ER-A19L TCGA-GN-A26A 
       10.26        24.00         4.93        11.15        12.99        12.16 
TCGA-GN-A26D 
       14.70 

$`9P LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 
       45.70        19.36         6.31        78.44         6.58        15.35 
TCGA-GN-A264 
       31.33 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             4.93              6.31 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            24.00             78.44 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            12.16             19.36 
[1] "4.9 - 24.0 (12.2)" "6.3 - 78.4 (19.4)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" 
[1] "hr=" "5"  
D27V2, continuous
                   vv
clus                DISTANT METASTASIS
  9P LOSS MUTATED                    1
  9P LOSS WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                          2
  9P LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                     6
  9P LOSS WILD-TYPE                   8
D27V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                      8
D27V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5    4
  9P LOSS WILD-TYPE    7    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               5                 7
  MALE                 4                 7
                   vv
clus                N0 N1 N1A N1B N2B N3
  9P LOSS MUTATED    3  0   1   3   0  1
  9P LOSS WILD-TYPE  8  1   1   0   2  1
D27V5, multiclass
D27V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  9P LOSS MUTATED         0        1        0         1         1         0
  9P LOSS WILD-TYPE       4        0        1         1         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED            1          1          2
  9P LOSS WILD-TYPE          1          1          2
D27V7, multiclass

Clustering(28) Variable = 9q loss mutation analysis
D28V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   1 3
  9Q LOSS WILD-TYPE 4 6
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                10 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                 6 
$`9Q LOSS MUTATED`
TCGA-DA-A1IA TCGA-EE-A29D TCGA-GN-A26A TCGA-GN-A26D 
        4.93        11.15        12.16        14.70 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        45.70        24.00        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 
       78.44         6.58        15.35        31.33 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             4.93              6.31 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            14.70             78.44 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           11.655            17.355 
[1] "4.9 - 14.7 (11.7)" "6.3 - 78.4 (17.4)"
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
[1] "hr=" "3.3"
D28V2, continuous
                   vv
clus                DISTANT METASTASIS
  9Q LOSS MUTATED                    1
  9Q LOSS WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                          2
  9Q LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                     3
  9Q LOSS WILD-TYPE                  11
D28V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D28V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4    2
  9Q LOSS WILD-TYPE    8    9
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               4                 8
  MALE                 2                 9
                   vv
clus                N0 N1 N1A N1B N2B N3
  9Q LOSS MUTATED    2  0   1   3   0  0
  9Q LOSS WILD-TYPE  9  1   1   0   2  2
D28V5, multiclass
D28V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  9Q LOSS MUTATED         0        1        0         0         1         0
  9Q LOSS WILD-TYPE       4        0        1         2         2         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED            1          1          1
  9Q LOSS WILD-TYPE          1          1          3
D28V7, multiclass

Clustering(29) Variable = 10p loss mutation analysis
D29V1, survival
                    sevent
clus2                0 1
  10P LOSS MUTATED   1 6
  10P LOSS WILD-TYPE 4 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 7                  7 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                  3 
$`10P LOSS MUTATED`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A17Z TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A264 
       24.00         4.93         6.31        12.99         6.58        31.33 
TCGA-GN-A26A 
       12.16 

$`10P LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A1A1 TCGA-GN-A261 
       10.26        45.70        19.36        11.15        78.44        15.35 
TCGA-GN-A26D 
       14.70 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.93              10.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             31.33              78.44 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.16              15.35 
[1] "4.9 - 31.3 (12.2)"  "10.3 - 78.4 (15.3)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10P LOSS MUTATED                    2
  10P LOSS WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                          2
  10P LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                     7
  10P LOSS WILD-TYPE                   7
D29V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                       7
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7    4
  10P LOSS WILD-TYPE    5    7
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                7                  5
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  10P LOSS MUTATED    4  0   2   1   1  1
  10P LOSS WILD-TYPE  7  1   0   2   1  1
D29V5, multiclass
D29V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  10P LOSS MUTATED         1        1        0         1         1         0
  10P LOSS WILD-TYPE       3        0        1         1         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS MUTATED            2          1          2
  10P LOSS WILD-TYPE          0          1          2
D29V7, multiclass

Clustering(30) Variable = 10q loss mutation analysis
D30V1, survival
                    sevent
clus2                0 1
  10Q LOSS MUTATED   0 6
  10Q LOSS WILD-TYPE 5 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                  8 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 6                  3 
$`10Q LOSS MUTATED`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-EE-A17Z TCGA-ER-A19L TCGA-GN-A264 TCGA-GN-A26A 
       24.00         4.93         6.31        12.99        31.33        12.16 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A3F2 TCGA-EE-A29D TCGA-ER-A1A1 TCGA-ER-A3ET 
       10.26        45.70        19.36        11.15        78.44         6.58 
TCGA-GN-A261 TCGA-GN-A26D 
       15.35        14.70 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              4.93               6.58 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             31.33              78.44 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            12.575             15.025 
[1] "4.9 - 31.3 (12.6)" "6.6 - 78.4 (15.0)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "3.1"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10Q LOSS MUTATED                    2
  10Q LOSS WILD-TYPE                  1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                          1
  10Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                     6
  10Q LOSS WILD-TYPE                   8
D30V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    4
  10Q LOSS WILD-TYPE    7    7
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                5                  7
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  10Q LOSS MUTATED    4  0   1   1   0  1
  10Q LOSS WILD-TYPE  7  1   1   2   2  1
D30V5, multiclass
D30V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  10Q LOSS MUTATED         1        1        0         1         1         0
  10Q LOSS WILD-TYPE       3        0        1         1         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED            1          1          1
  10Q LOSS WILD-TYPE          1          1          3
D30V7, multiclass

Clustering(31) Variable = 11p loss mutation analysis
D31V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   0 5
  11P LOSS WILD-TYPE 5 4
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  9 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  4 
$`11P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29D TCGA-ER-A19L TCGA-GN-A264 TCGA-GN-A26A 
       10.26        11.15        12.99        31.33        12.16 

$`11P LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 
       45.70        24.00         4.93        19.36         6.31        78.44 
TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26D 
        6.58        15.35        14.70 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             10.26               4.93 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             31.33              78.44 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             12.16              15.35 
[1] "10.3 - 31.3 (12.2)" "4.9 - 78.4 (15.3)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11P LOSS MUTATED                    0
  11P LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                          1
  11P LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                     5
  11P LOSS WILD-TYPE                   9
D31V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       9
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    4
  11P LOSS WILD-TYPE   10    7
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                2                 10
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  11P LOSS MUTATED    2  0   1   1   0  0
  11P LOSS WILD-TYPE  9  1   1   2   2  2
D31V5, multiclass
D31V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  11P LOSS MUTATED         1        0        0         1         0         0
  11P LOSS WILD-TYPE       3        1        1         1         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS MUTATED            1          0          1
  11P LOSS WILD-TYPE          1          2          3
D31V7, multiclass

Clustering(32) Variable = 11q loss mutation analysis
D32V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   1 5
  11Q LOSS WILD-TYPE 4 4
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                  8 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  4 
$`11Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29D TCGA-ER-A19L TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       10.26        11.15        12.99        31.33        12.16        14.70 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A1A1 
       45.70        24.00         4.93        19.36         6.31        78.44 
TCGA-ER-A3ET TCGA-GN-A261 
        6.58        15.35 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             10.26               4.93 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             31.33              78.44 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            12.575             17.355 
[1] "10.3 - 31.3 (12.6)" "4.9 - 78.4 (17.4)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
[1] "hr=" "2"  
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11Q LOSS MUTATED                    1
  11Q LOSS WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          1
  11Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                     6
  11Q LOSS WILD-TYPE                   8
D32V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4    4
  11Q LOSS WILD-TYPE    8    7
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                4                  8
  MALE                  4                  7
                    vv
clus                 N0 N1 N1A N1B N2B N3
  11Q LOSS MUTATED    4  0   1   1   0  0
  11Q LOSS WILD-TYPE  7  1   1   2   2  2
D32V5, multiclass
D32V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  11Q LOSS MUTATED         1        0        0         1         2         0
  11Q LOSS WILD-TYPE       3        1        1         1         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED            1          0          1
  11Q LOSS WILD-TYPE          1          2          3
D32V7, multiclass

Clustering(33) Variable = 12q loss mutation analysis
D33V1, survival
                    sevent
clus2                0 1
  12Q LOSS MUTATED   2 1
  12Q LOSS WILD-TYPE 3 8
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 11 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                  8 
$`12Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-GN-A26D 
       10.26        45.70        14.70 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       24.00         4.93        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       78.44         6.58        15.35        31.33        12.16 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             10.26               4.93 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             45.70              78.44 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             14.70              12.99 
[1] "10.3 - 45.7 (14.7)" "4.9 - 78.4 (13.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
[1] "hr=" "2.5"
D33V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12Q LOSS MUTATED                    0
  12Q LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          1
  12Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     2
  12Q LOSS WILD-TYPE                  12
D33V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      12
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   10   10
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 10
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  12Q LOSS MUTATED    3  0   0   0   0  0
  12Q LOSS WILD-TYPE  8  1   2   3   2  2
D33V5, multiclass
D33V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  12Q LOSS MUTATED         0        0        0         1         2         0
  12Q LOSS WILD-TYPE       4        1        1         1         1         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  12Q LOSS MUTATED            0          0          0
  12Q LOSS WILD-TYPE          2          2          4
D33V7, multiclass

Clustering(34) Variable = 13q loss mutation analysis
D34V1, survival
                    sevent
clus2                0 1
  13Q LOSS MUTATED   1 1
  13Q LOSS WILD-TYPE 4 8
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 12 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  8 
$`13Q LOSS MUTATED`
TCGA-EE-A29D TCGA-GN-A26D 
       11.15        14.70 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       12.99        78.44         6.58        15.35        31.33        12.16 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             11.15               4.93 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             14.70              78.44 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            12.925             14.170 
[1] "11.2 - 14.7 (12.9)" "4.9 - 78.4 (14.2)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS
  13Q LOSS MUTATED                    0
  13Q LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          1
  13Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                     3
  13Q LOSS WILD-TYPE                  11
D34V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      11
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    1
  13Q LOSS WILD-TYPE    9   10
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                3                  9
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  13Q LOSS MUTATED    2  0   0   2   0  0
  13Q LOSS WILD-TYPE  9  1   2   1   2  2
D34V5, multiclass
D34V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  13Q LOSS MUTATED         1        0        0         0         1         0
  13Q LOSS WILD-TYPE       3        1        1         2         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED            0          0          1
  13Q LOSS WILD-TYPE          2          2          3
D34V7, multiclass

Clustering(35) Variable = 14q loss mutation analysis
D35V1, survival
                    sevent
clus2                0 1
  14Q LOSS MUTATED   1 3
  14Q LOSS WILD-TYPE 4 6
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 10 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                  6 
$`14Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-GN-A264 TCGA-GN-A26A 
       10.26        45.70        31.33        12.16 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-ER-A19L 
       24.00         4.93        19.36         6.31        11.15        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A26D 
       78.44         6.58        15.35        14.70 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.26               4.93 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             45.70              78.44 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            21.745             13.845 
[1] "10.3 - 45.7 (21.7)" "4.9 - 78.4 (13.8)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 DISTANT METASTASIS
  14Q LOSS MUTATED                    0
  14Q LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                          3
  14Q LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                     2
  14Q LOSS WILD-TYPE                  12
D35V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      12
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    2
  14Q LOSS WILD-TYPE    9    9
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                3                  9
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  14Q LOSS MUTATED    2  0   1   1   0  0
  14Q LOSS WILD-TYPE  9  1   1   2   2  2
D35V5, multiclass
D35V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  14Q LOSS MUTATED         0        0        0         1         1         0
  14Q LOSS WILD-TYPE       4        1        1         1         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED            1          0          0
  14Q LOSS WILD-TYPE          1          2          4
D35V7, multiclass

Clustering(36) Variable = 16q loss mutation analysis
D36V1, survival
                    sevent
clus2                0 1
  16Q LOSS MUTATED   0 2
  16Q LOSS WILD-TYPE 5 7
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 12 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                  7 
$`16Q LOSS MUTATED`
TCGA-EE-A17Z TCGA-EE-A29D 
        6.31        11.15 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-ER-A19L 
       10.26        45.70        24.00         4.93        19.36        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       78.44         6.58        15.35        31.33        12.16        14.70 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              6.31               4.93 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.15              78.44 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             8.730             15.025 
[1] "6.3 - 11.2 (8.7)"  "4.9 - 78.4 (15.0)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-ER-A19L 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-GN-A261 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D36V2, continuous
                    vv
clus                 DISTANT METASTASIS
  16Q LOSS MUTATED                    1
  16Q LOSS WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          1
  16Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                     2
  16Q LOSS WILD-TYPE                  12
D36V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      12
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    2
  16Q LOSS WILD-TYPE   10    9
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                2                 10
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  16Q LOSS MUTATED    2  0   0   2   0  0
  16Q LOSS WILD-TYPE  9  1   2   1   2  2
D36V5, multiclass
D36V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  16Q LOSS MUTATED         0        0        0         1         1         0
  16Q LOSS WILD-TYPE       4        1        1         1         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED            0          0          1
  16Q LOSS WILD-TYPE          2          2          3
D36V7, multiclass

Clustering(37) Variable = 17p loss mutation analysis
D37V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   0 1
  17P LOSS WILD-TYPE 5 8
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  8 
$`17P LOSS MUTATED`
TCGA-D3-A2J6 
       10.26 

$`17P LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       45.70        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A 
       12.99        78.44         6.58        15.35        31.33        12.16 
TCGA-GN-A26D 
       14.70 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.26               4.93 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.26              78.44 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.26              14.70 
[1] "10.3 - 10.3 (10.3)" "4.9 - 78.4 (14.7)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 13 
        TCGA-D3-A3CC         TCGA-D3-A3CF         TCGA-DA-A1IA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-EE-A17Z         TCGA-EE-A29D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17P LOSS WILD-TYPE" 
D37V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17P LOSS MUTATED                    0
  17P LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          0
  17P LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                     3
  17P LOSS WILD-TYPE                  11
D37V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      11
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    2
  17P LOSS WILD-TYPE   11    9
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                1                 11
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  17P LOSS MUTATED    3  0   0   0   0  0
  17P LOSS WILD-TYPE  8  1   2   3   2  2
D37V5, multiclass
D37V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  17P LOSS MUTATED         1        1        0         1         0         0
  17P LOSS WILD-TYPE       3        0        1         1         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS MUTATED            0          0          0
  17P LOSS WILD-TYPE          2          2          4
D37V7, multiclass

Clustering(38) Variable = 17q loss mutation analysis
D38V1, survival
                    sevent
clus2                0 1
  17Q LOSS MUTATED   0 2
  17Q LOSS WILD-TYPE 5 7
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 12 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                  7 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-ER-A19L 
       10.26        12.99 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       45.70        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       78.44         6.58        15.35        31.33        12.16        14.70 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             10.26               4.93 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             12.99              78.44 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            11.625             15.025 
[1] "10.3 - 13.0 (11.6)" "4.9 - 78.4 (15.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 12 
        TCGA-D3-A3CC         TCGA-D3-A3CF         TCGA-DA-A1IA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-EE-A17Z         TCGA-EE-A29D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-GN-A261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D38V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17Q LOSS MUTATED                    0
  17Q LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          0
  17Q LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                     3
  17Q LOSS WILD-TYPE                  11
D38V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      11
D38V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0    3
  17Q LOSS WILD-TYPE   12    8
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                0                 12
  MALE                  3                  8
                    vv
clus                 N0 N1 N1A N1B N2B N3
  17Q LOSS MUTATED    2  0   0   0   0  0
  17Q LOSS WILD-TYPE  9  1   2   3   2  2
D38V5, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 19 
        TCGA-D3-A3CC         TCGA-D3-A3CF         TCGA-D9-A149 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A2GK         TCGA-EE-A2MR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-FS-A1Z4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZG         TCGA-FS-A1ZJ         TCGA-FS-A1ZK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZU         TCGA-GN-A261         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" 
D38V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  17Q LOSS MUTATED         0        1        0         1         0         0
  17Q LOSS WILD-TYPE       4        0        1         1         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS MUTATED            0          0          0
  17Q LOSS WILD-TYPE          2          2          4
D38V7, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 18 
        TCGA-D3-A3CC         TCGA-D3-A3CF         TCGA-DA-A1IA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-EE-A17Z         TCGA-EE-A29D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2GK         TCGA-EE-A2MR         TCGA-ER-A1A1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-FS-A1Z4         TCGA-FS-A1ZG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZJ         TCGA-FS-A1ZK         TCGA-FS-A1ZU 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 

Clustering(39) Variable = 18q loss mutation analysis
D39V1, survival
                    sevent
clus2                0 1
  18Q LOSS MUTATED   0 2
  18Q LOSS WILD-TYPE 5 7
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 12 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  7 
$`18Q LOSS MUTATED`
TCGA-DA-A1IA TCGA-EE-A29D 
        4.93        11.15 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       10.26        45.70        24.00        19.36         6.31        12.99 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       78.44         6.58        15.35        31.33        12.16        14.70 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              4.93               6.31 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             11.15              78.44 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             8.040             15.025 
[1] "4.9 - 11.2 (8.0)"  "6.3 - 78.4 (15.0)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-EE-A17Z         TCGA-ER-A19L 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-GN-A261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D39V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18Q LOSS MUTATED                    1
  18Q LOSS WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          0
  18Q LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                     2
  18Q LOSS WILD-TYPE                  12
D39V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      12
D39V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    2
  18Q LOSS WILD-TYPE   11    9
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                1                 11
  MALE                  2                  9
                    vv
clus                 N0 N1 N1A N1B N2B N3
  18Q LOSS MUTATED    1  0   0   2   0  0
  18Q LOSS WILD-TYPE 10  1   2   1   2  2
D39V5, multiclass
D39V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  18Q LOSS MUTATED         0        1        0         0         0         0
  18Q LOSS WILD-TYPE       4        0        1         2         3         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED            0          1          1
  18Q LOSS WILD-TYPE          2          1          3
D39V7, multiclass

Clustering(40) Variable = 21q loss mutation analysis
D40V1, survival
                    sevent
clus2                0 1
  21Q LOSS WILD-TYPE 5 9
21Q LOSS WILD-TYPE 
                14 
[1] 9
$`21Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-EE-A29D TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 
       11.15        12.99        78.44         6.58        15.35        31.33 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

21Q LOSS WILD-TYPE 
              4.93 
21Q LOSS WILD-TYPE 
             78.44 
21Q LOSS WILD-TYPE 
            13.845 
[1] "4.9 - 78.4 (13.8)"
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D40V2, continuous
                    vv
clus                 DISTANT METASTASIS
  21Q LOSS MUTATED                    1
  21Q LOSS WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          0
  21Q LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                     2
  21Q LOSS WILD-TYPE                  12
D40V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      12
D40V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2    1
  21Q LOSS WILD-TYPE   10   10
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                2                 10
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  21Q LOSS MUTATED    2  0   0   0   1  0
  21Q LOSS WILD-TYPE  9  1   2   3   1  2
D40V5, multiclass
D40V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  21Q LOSS MUTATED         0        1        0         0         1         0
  21Q LOSS WILD-TYPE       4        0        1         2         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  21Q LOSS MUTATED            0          0          1
  21Q LOSS WILD-TYPE          2          2          3
D40V7, 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")
