
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-NRAS_Hotspot_Mutants/3164410/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NRAS_Hotspot_Mutants/3215657/SKCM-NRAS_Hotspot_Mutants.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-NRAS_Hotspot_Mutants", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                           "-oT=SKCM-NRAS_Hotspot_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=45, in cluster file=62, common to both=45
[1] "Reduce the number of clustering variables from 80 to 58."
[1] 58 45
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                38 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                38 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24                21 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24                21 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                38 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                38 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                38 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                38 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                40 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                40 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                40 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                40 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                42 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                42 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                42 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                42 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21                24 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21                24 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                36 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                9                36 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                7                38 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                34 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                34 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               16                29 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               16                29 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 41 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 41 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 41 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 41 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 42 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                 42 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                16                 29 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                16                 29 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 41 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 41 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 39 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 39 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 39 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 39 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 40 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 40 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 42 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 42 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 38 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 41 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 41 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 41 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 41 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 40 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 40 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 39 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 39 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 35 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 35 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 32 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 32 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 38 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 38 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                 35 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                10                 35 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                40 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                40 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                39 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                39 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10                35 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10                35 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                33 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                33 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                39 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                39 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                23 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                23 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                37 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                37 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28                17 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               28                17 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                23 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                23 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 26 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 25 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                20                 25 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                 30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                15                 30 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                 29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                 29 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 39 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 39 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 36 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 36 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                 41 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 4                 41 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                12                 33 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                12                 33 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 41 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 41 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 37 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                 37 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                15                 30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                15                 30 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 42 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 42 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 36 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 36 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 37 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 37 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 39 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 39 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 41 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 41 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 41 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 41 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 40 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 40 
[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 45 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
          NA           NA           NA          164         1484         1192 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
          NA           NA           NA           NA          247          269 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
         304           NA           NA          769          727           NA 
TCGA-EE-A2GD TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GU TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AC TCGA-ER-A19D TCGA-ER-A19N TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
          NA           NA         1303           NA           NA           NA 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZT TCGA-FS-A1ZW 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZY TCGA-GN-A267 TCGA-GN-A268 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=21,	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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
 T0 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B  TX 
  4   4   2   4   5   3   1   5   4   1   2   6   1 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 45 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=28, 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=13, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    0  2
  1P GAIN WILD-TYPE  9 11
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                20 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                11 
$`1P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-EE-A29L 
        8.38         1.08 

$`1P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.08              2.43 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             8.38             48.79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             4.73             10.78 
[1] "1.1 - 8.4 (4.7)"   "2.4 - 48.8 (10.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A3MV        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29V 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, continuous
                   vv
clus                DISTANT METASTASIS
  1P GAIN MUTATED                    1
  1P GAIN WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          2
  1P GAIN WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                     4
  1P GAIN WILD-TYPE                  24
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                                                                                    4
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     24
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    4
  1P GAIN WILD-TYPE   13   25
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                13
  MALE                 4                25
                   vv
clus                N0 N1A N1B N2A N2B N3
  1P GAIN MUTATED    5   1   0   0   0  1
  1P GAIN WILD-TYPE 22   2   4   1   2  4
D1V5, multiclass
D1V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P GAIN MUTATED             0       1        1        1        1         0
  1P GAIN WILD-TYPE           1       2        3        5        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P GAIN MUTATED           0         1         0          0          1
  1P GAIN WILD-TYPE         4         1         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  1P GAIN MUTATED            1        0
  1P GAIN WILD-TYPE          5        1
D1V7, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2               0 1
  1Q GAIN MUTATED   6 6
  1Q GAIN WILD-TYPE 3 7
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                10 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 7 
$`1Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A29L 
       16.47         8.38         5.39        39.19         7.00         1.08 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-GN-A267 
        8.84         9.99        25.28        23.90         3.52        16.21 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29V 
       28.08        48.79        11.57         4.27         8.12         2.43 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A268 
        8.09         9.67        42.84        15.39 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.08              2.43 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            39.19             48.79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            9.415            10.620 
[1] "1.1 - 39.2 (9.4)"  "2.4 - 48.8 (10.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS
  1Q GAIN MUTATED                    4
  1Q GAIN WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                          6
  1Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    14
  1Q GAIN WILD-TYPE                  14
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   14
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     14
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      9   15
  1Q GAIN WILD-TYPE    7   14
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               9                 7
  MALE                15                14
                   vv
clus                N0 N1A N1B N2A N2B N3
  1Q GAIN MUTATED   13   1   3   1   1  3
  1Q GAIN WILD-TYPE 14   2   1   0   1  2
D2V5, multiclass
D2V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q GAIN MUTATED             0       1        2        3        2         2
  1Q GAIN WILD-TYPE           1       2        2        3        2         1
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED           2         1         1          1          3
  1Q GAIN WILD-TYPE         2         1         0          0          3
                   vv
clus                STAGE IIIC STAGE IV
  1Q GAIN MUTATED            4        0
  1Q GAIN WILD-TYPE          2        1
D2V7, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  2
  2P GAIN WILD-TYPE  6 11
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                17 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                11 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N 
       16.47         5.39         1.08         8.84        42.84 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        4.27         8.12         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        16.21        15.39 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.08              2.43 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            42.84             48.79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.84              9.99 
[1] "1.1 - 42.8 (8.8)"  "2.4 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS
  2P GAIN MUTATED                    0
  2P GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P GAIN MUTATED                                                                                          3
  2P GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                     4
  2P GAIN WILD-TYPE                  24
D3V3, multiclass
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     24
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    3
  2P GAIN WILD-TYPE   12   26
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               4                12
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  2P GAIN MUTATED    2   0   1   1   0  2
  2P GAIN WILD-TYPE 25   3   3   0   2  3
D3V5, multiclass
D3V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P GAIN MUTATED             0       0        0        0        0         1
  2P GAIN WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P GAIN MUTATED           0         1         0          0          1
  2P GAIN WILD-TYPE         4         1         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  2P GAIN MUTATED            3        0
  2P GAIN WILD-TYPE          3        1
D3V7, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    3  2
  2Q GAIN WILD-TYPE  6 11
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                17 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                11 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N 
       16.47         5.39         1.08         8.84        42.84 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        4.27         8.12         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        16.21        15.39 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.08              2.43 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            42.84             48.79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.84              9.99 
[1] "1.1 - 42.8 (8.8)"  "2.4 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS
  2Q GAIN MUTATED                    0
  2Q GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q GAIN MUTATED                                                                                          3
  2Q GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                     4
  2Q GAIN WILD-TYPE                  24
D4V3, multiclass
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     24
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    3
  2Q GAIN WILD-TYPE   12   26
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                12
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  2Q GAIN MUTATED    2   0   1   1   0  2
  2Q GAIN WILD-TYPE 25   3   3   0   2  3
D4V5, multiclass
D4V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q GAIN MUTATED             0       0        0        0        0         1
  2Q GAIN WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED           0         1         0          0          1
  2Q GAIN WILD-TYPE         4         1         1          1          5
                   vv
clus                STAGE IIIC STAGE IV
  2Q GAIN MUTATED            3        0
  2Q GAIN WILD-TYPE          3        1
D4V7, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE  7 12
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                19 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                12 
$`3P GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A29L TCGA-EE-A29R 
        5.39         1.08         8.84 

$`3P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              2.43 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             8.84             48.79 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             5.39             11.57 
[1] "1.1 - 8.8 (5.4)"   "2.4 - 48.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS
  3P GAIN MUTATED                    0
  3P GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          3
  3P GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     2
  3P GAIN WILD-TYPE                  26
D5V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     26
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    3
  3P GAIN WILD-TYPE   14   26
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  3P GAIN MUTATED    1   1   1   1   0  1
  3P GAIN WILD-TYPE 26   2   3   0   2  4
D5V5, multiclass
D5V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P GAIN MUTATED             0       0        0        0        0         1
  3P GAIN WILD-TYPE           1       3        4        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P GAIN MUTATED           0         0         0          0          2
  3P GAIN WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  3P GAIN MUTATED            2        0
  3P GAIN WILD-TYPE          4        1
D5V7, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2  0
  3Q GAIN WILD-TYPE  7 13
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                13 
$`3Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A29R 
        5.39         8.84 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5.39              1.08 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             8.84             48.79 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            7.115            10.780 
[1] "5.4 - 8.8 (7.1)"   "1.1 - 48.8 (10.8)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-DA-A1HV 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29S        TCGA-EE-A29V 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D6V2, continuous
                   vv
clus                DISTANT METASTASIS
  3Q GAIN MUTATED                    0
  3Q GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          3
  3Q GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     2
  3Q GAIN WILD-TYPE                  26
D6V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     26
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    3
  3Q GAIN WILD-TYPE   14   26
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                14
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  3Q GAIN MUTATED    2   1   1   1   0  0
  3Q GAIN WILD-TYPE 25   2   3   0   2  5
D6V5, multiclass
D6V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q GAIN MUTATED             0       0        0        0        1         1
  3Q GAIN WILD-TYPE           1       3        4        6        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q GAIN MUTATED           0         0         0          0          2
  3Q GAIN WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  3Q GAIN MUTATED            1        0
  3Q GAIN WILD-TYPE          5        1
D6V7, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    2  0
  4P GAIN WILD-TYPE  7 13
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                20 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                13 
$`4P GAIN MUTATED`
TCGA-DA-A1HV TCGA-DA-A1I1 
       48.79        39.19 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38         5.39         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            39.19              1.08 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            48.79             42.84 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           43.990             9.255 
[1] "39.2 - 48.8 (44.0)" "1.1 - 42.8 (9.3)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4P GAIN MUTATED"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185        TCGA-EE-A29L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29V 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
D7V2, continuous
                   vv
clus                DISTANT METASTASIS
  4P GAIN MUTATED                    0
  4P GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          2
  4P GAIN WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                     1
  4P GAIN WILD-TYPE                  27
D7V3, multiclass
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     27
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    2
  4P GAIN WILD-TYPE   15   27
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                15
  MALE                 2                27
                   vv
clus                N0 N1A N1B N2A N2B N3
  4P GAIN MUTATED    0   1   0   0   1  1
  4P GAIN WILD-TYPE 27   2   4   1   1  4
D7V5, multiclass
D7V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P GAIN MUTATED             0       0        0        0        0         0
  4P GAIN WILD-TYPE           1       3        4        6        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P GAIN MUTATED           0         0         0          0          2
  4P GAIN WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  4P GAIN MUTATED            1        0
  4P GAIN WILD-TYPE          5        1
D7V7, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    2  0
  4Q GAIN WILD-TYPE  7 13
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                20 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                13 
$`4Q GAIN MUTATED`
TCGA-DA-A1HV TCGA-DA-A1I1 
       48.79        39.19 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38         5.39         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            39.19              1.08 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            48.79             42.84 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           43.990             9.255 
[1] "39.2 - 48.8 (44.0)" "1.1 - 42.8 (9.3)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "4Q GAIN MUTATED"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                20 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185        TCGA-EE-A29L 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29V 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D8V2, continuous
                   vv
clus                DISTANT METASTASIS
  4Q GAIN MUTATED                    0
  4Q GAIN WILD-TYPE                  8
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          2
  4Q GAIN WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                     1
  4Q GAIN WILD-TYPE                  27
D8V3, multiclass
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     27
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   15   27
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                15
  MALE                 2                27
                   vv
clus                N0 N1A N1B N2A N2B N3
  4Q GAIN MUTATED    0   1   0   0   1  1
  4Q GAIN WILD-TYPE 27   2   4   1   1  4
D8V5, multiclass
D8V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q GAIN MUTATED             0       0        0        0        0         0
  4Q GAIN WILD-TYPE           1       3        4        6        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q GAIN MUTATED           0         0         0          0          2
  4Q GAIN WILD-TYPE         4         2         1          1          4
                   vv
clus                STAGE IIIC STAGE IV
  4Q GAIN MUTATED            1        0
  4Q GAIN WILD-TYPE          5        1
D8V7, multiclass

Clustering(9) Variable = 6p gain mutation analysis
D9V1, survival
                   sevent
clus2               0 1
  6P GAIN MUTATED   5 4
  6P GAIN WILD-TYPE 4 9
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9                13 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                 9 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29R 
       16.47        48.79        39.19         7.00         4.27         8.84 
TCGA-EE-A29S TCGA-EE-A2A5 TCGA-ER-A19N 
        9.99         9.67        42.84 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q 
       28.08         8.38         5.39        11.57         1.08         8.12 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-GN-A267 
        2.43         8.09        25.28        23.90         3.52        16.21 
TCGA-GN-A268 
       15.39 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.27              1.08 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            48.79             28.08 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             9.99              8.38 
[1] "4.3 - 48.8 (10.0)" "1.1 - 28.1 (8.4)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS
  6P GAIN MUTATED                    4
  6P GAIN WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          5
  6P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    12
  6P GAIN WILD-TYPE                  16
D9V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     16
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9   12
  6P GAIN WILD-TYPE    7   17
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               9                 7
  MALE                12                17
                   vv
clus                N0 N1A N1B N2A N2B N3
  6P GAIN MUTATED   12   1   1   0   2  3
  6P GAIN WILD-TYPE 15   2   3   1   0  2
D9V5, multiclass
D9V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             0       2        3        1        1         2
  6P GAIN WILD-TYPE           1       1        1        5        3         1
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P GAIN MUTATED           2         1         0          0          3
  6P GAIN WILD-TYPE         2         1         1          1          3
                   vv
clus                STAGE IIIC STAGE IV
  6P GAIN MUTATED            4        0
  6P GAIN WILD-TYPE          2        1
D9V7, multiclass

Clustering(10) Variable = 7p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    1  2
  7P GAIN WILD-TYPE  8 11
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                3                19 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                11 
$`7P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-GN-A267 
       16.47        48.79        16.21 

$`7P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A268 
       15.39 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            16.21              1.08 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            48.79             42.84 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            16.47              8.84 
[1] "16.2 - 48.8 (16.5)" "1.1 - 42.8 (8.8)"  
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D10V2, continuous
                   vv
clus                DISTANT METASTASIS
  7P GAIN MUTATED                    1
  7P GAIN WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                          3
  7P GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                     5
  7P GAIN WILD-TYPE                  23
D10V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     23
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      3    6
  7P GAIN WILD-TYPE   13   23
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               3                13
  MALE                 6                23
                   vv
clus                N0 N1A N1B N2A N2B N3
  7P GAIN MUTATED    5   2   0   0   1  1
  7P GAIN WILD-TYPE 22   1   4   1   1  4
D10V5, multiclass
D10V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             0       1        1        0        0         1
  7P GAIN WILD-TYPE           1       2        3        6        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P GAIN MUTATED           1         1         0          1          2
  7P GAIN WILD-TYPE         3         1         1          0          4
                   vv
clus                STAGE IIIC STAGE IV
  7P GAIN MUTATED            1        0
  7P GAIN WILD-TYPE          5        1
D10V7, multiclass

Clustering(11) Variable = 7q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    2  2
  7Q GAIN WILD-TYPE  7 11
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                18 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                11 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-GN-A267 
       16.47         5.39        48.79        16.21 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38        39.19         7.00        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        1.08         8.12         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
       25.28        23.90         9.67         3.52        42.84        15.39 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             5.39              1.08 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            48.79             42.84 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           16.340             9.255 
[1] "5.4 - 48.8 (16.3)" "1.1 - 42.8 (9.3)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS
  7Q GAIN MUTATED                    1
  7Q GAIN WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                          3
  7Q GAIN WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                     3
  7Q GAIN WILD-TYPE                  25
D11V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                     25
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    3
  7Q GAIN WILD-TYPE   12   26
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               4                12
  MALE                 3                26
                   vv
clus                N0 N1A N1B N2A N2B N3
  7Q GAIN MUTATED    2   2   0   1   1  1
  7Q GAIN WILD-TYPE 25   1   4   0   1  4
D11V5, multiclass
D11V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             0       0        0        0        0         0
  7Q GAIN WILD-TYPE           1       3        4        6        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED           1         1         0          1          3
  7Q GAIN WILD-TYPE         3         1         1          0          3
                   vv
clus                STAGE IIIC STAGE IV
  7Q GAIN MUTATED            1        0
  7Q GAIN WILD-TYPE          5        1
D11V7, multiclass

Clustering(12) Variable = 8p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    4  1
  8P GAIN WILD-TYPE  5 12
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                17 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                12 
$`8P GAIN MUTATED`
TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-EE-A29R TCGA-ER-A19N TCGA-GN-A267 
        5.39        39.19         8.84        42.84        16.21 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47        28.08         8.38        48.79         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         1.08         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A268 
       25.28        23.90         9.67         3.52        15.39 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.39              1.08 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            42.84             48.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            16.21              9.67 
[1] "5.4 - 42.8 (16.2)" "1.1 - 48.8 (9.7)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
[1] "hr=" "5.1"
D12V2, continuous
                   vv
clus                DISTANT METASTASIS
  8P GAIN MUTATED                    1
  8P GAIN WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                          5
  8P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                     5
  8P GAIN WILD-TYPE                  23
D12V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     23
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    8
  8P GAIN WILD-TYPE   13   21
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               3                13
  MALE                 8                21
                   vv
clus                N0 N1A N1B N2A N2B N3
  8P GAIN MUTATED    5   2   1   1   0  1
  8P GAIN WILD-TYPE 22   1   3   0   2  4
D12V5, multiclass
D12V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P GAIN MUTATED             0       0        0        1        1         1
  8P GAIN WILD-TYPE           1       3        4        5        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P GAIN MUTATED           1         1         0          1          2
  8P GAIN WILD-TYPE         3         1         1          0          4
                   vv
clus                STAGE IIIC STAGE IV
  8P GAIN MUTATED            2        0
  8P GAIN WILD-TYPE          4        1
D12V7, multiclass

Clustering(13) Variable = 8q gain mutation analysis
D13V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   4 4
  8Q GAIN WILD-TYPE 5 9
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                8                14 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                 9 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A29R TCGA-EE-A2A5 
       16.47         5.39        39.19         7.00         8.84         9.67 
TCGA-ER-A19N TCGA-GN-A267 
       42.84        16.21 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L 
       28.08         8.38        48.79        11.57         4.27         1.08 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.12         9.99         2.43         8.09        25.28        23.90 
TCGA-ER-A19D TCGA-GN-A268 
        3.52        15.39 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             5.39              1.08 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            42.84             48.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.940             9.185 
[1] "5.4 - 42.8 (12.9)" "1.1 - 48.8 (9.2)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D13V2, continuous
                   vv
clus                DISTANT METASTASIS
  8Q GAIN MUTATED                    2
  8Q GAIN WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                          6
  8Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                     8
  8Q GAIN WILD-TYPE                  20
D13V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     20
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5   11
  8Q GAIN WILD-TYPE   11   18
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                11
  MALE                11                18
                   vv
clus                N0 N1A N1B N2A N2B N3
  8Q GAIN MUTATED    8   2   1   1   1  2
  8Q GAIN WILD-TYPE 19   1   3   0   1  3
D13V5, multiclass
D13V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q GAIN MUTATED             0       1        1        2        1         1
  8Q GAIN WILD-TYPE           1       2        3        4        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED           1         1         0          1          3
  8Q GAIN WILD-TYPE         3         1         1          0          3
                   vv
clus                STAGE IIIC STAGE IV
  8Q GAIN MUTATED            3        0
  8Q GAIN WILD-TYPE          3        1
D13V7, multiclass

Clustering(14) Variable = 11p gain mutation analysis
D14V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE  8 12
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 20 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 12 
$`11P GAIN MUTATED`
TCGA-DA-A3F3 TCGA-ER-A19N 
        7.00        42.84 

$`11P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              7.00               1.08 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             42.84              48.79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             24.92               9.83 
[1] "7.0 - 42.8 (24.9)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
D14V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11P GAIN MUTATED                    1
  11P GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P GAIN MUTATED                                                                                          1
  11P GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                     2
  11P GAIN WILD-TYPE                  26
D14V3, multiclass
                                                                                          clus
vv                                                                                         11P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      26
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    4
  11P GAIN WILD-TYPE   16   25
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                0                 16
  MALE                  4                 25
                    vv
clus                 N0 N1A N1B N2A N2B N3
  11P GAIN MUTATED    1   1   0   0   1  0
  11P GAIN WILD-TYPE 26   2   4   1   1  5
D14V5, multiclass
D14V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P GAIN MUTATED             0       0        0        0        1         0
  11P GAIN WILD-TYPE           1       3        4        6        3         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED           0         0         0          0          2
  11P GAIN WILD-TYPE         4         2         1          1          4
                    vv
clus                 STAGE IIIC STAGE IV
  11P GAIN MUTATED            0        0
  11P GAIN WILD-TYPE          6        1
D14V7, multiclass

Clustering(15) Variable = 11q gain mutation analysis
D15V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  1
  11Q GAIN WILD-TYPE  8 12
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 20 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 12 
$`11Q GAIN MUTATED`
TCGA-DA-A3F3 TCGA-ER-A19N 
        7.00        42.84 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               1.08 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             42.84              48.79 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             24.92               9.83 
[1] "7.0 - 42.8 (24.9)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"11Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D15V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11Q GAIN MUTATED                    1
  11Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q GAIN MUTATED                                                                                          1
  11Q GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                     2
  11Q GAIN WILD-TYPE                  26
D15V3, multiclass
                                                                                          clus
vv                                                                                         11Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      26
D15V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0    4
  11Q GAIN WILD-TYPE   16   25
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                0                 16
  MALE                  4                 25
                    vv
clus                 N0 N1A N1B N2A N2B N3
  11Q GAIN MUTATED    1   1   0   0   1  0
  11Q GAIN WILD-TYPE 26   2   4   1   1  5
D15V5, multiclass
D15V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q GAIN MUTATED             0       0        0        0        1         0
  11Q GAIN WILD-TYPE           1       3        4        6        3         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED           0         0         0          0          2
  11Q GAIN WILD-TYPE         4         2         1          1          4
                    vv
clus                 STAGE IIIC STAGE IV
  11Q GAIN MUTATED            0        0
  11Q GAIN WILD-TYPE          6        1
D15V7, multiclass

Clustering(16) Variable = 12p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    1  1
  12P GAIN WILD-TYPE  8 12
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 20 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                 12 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV 
       16.47         5.39 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              5.39               1.08 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             16.47              48.79 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             10.93               9.83 
[1] "5.4 - 16.5 (10.9)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"12P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q8         TCGA-D3-A2J8         TCGA-DA-A1HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A3F3         TCGA-EE-A17X 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A29L         TCGA-EE-A29Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A1         TCGA-EE-A2A2 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D16V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12P GAIN MUTATED                    0
  12P GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          1
  12P GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                     2
  12P GAIN WILD-TYPE                  26
D16V3, multiclass
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      26
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    0
  12P GAIN WILD-TYPE   13   29
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  0                 29
                    vv
clus                 N0 N1A N1B N2A N2B N3
  12P GAIN MUTATED    1   0   0   1   0  1
  12P GAIN WILD-TYPE 26   3   4   0   2  4
D16V5, multiclass
D16V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P GAIN MUTATED             0       0        1        0        0         0
  12P GAIN WILD-TYPE           1       3        3        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED           0         0         0          0          1
  12P GAIN WILD-TYPE         4         2         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  12P GAIN MUTATED            1        0
  12P GAIN WILD-TYPE          5        1
D16V7, multiclass

Clustering(17) Variable = 13q gain mutation analysis
D17V1, survival
                    sevent
clus2                0 1
  13Q GAIN MUTATED   2 5
  13Q GAIN WILD-TYPE 7 8
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                 15 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                  8 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A3F3 TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 
       16.47         7.00         8.84         9.67        42.84        16.21 
TCGA-GN-A268 
       15.39 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A17X 
       28.08         8.38         5.39        48.79        39.19        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         1.08         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D 
       25.28        23.90         3.52 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.00               1.08 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             42.84              48.79 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             15.39               8.38 
[1] "7.0 - 42.8 (15.4)" "1.1 - 48.8 (8.4)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A268 
  "13Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A268 
  "13Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A268 
  "13Q GAIN MUTATED" 
[1] "hr=" "1.1"
D17V2, continuous
                    vv
clus                 DISTANT METASTASIS
  13Q GAIN MUTATED                    5
  13Q GAIN WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q GAIN MUTATED                                                                                          4
  13Q GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                     7
  13Q GAIN WILD-TYPE                  21
D17V3, multiclass
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      21
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   10
  13Q GAIN WILD-TYPE   10   19
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                6                 10
  MALE                 10                 19
                    vv
clus                 N0 N1A N1B N2A N2B N3
  13Q GAIN MUTATED    8   2   2   0   1  1
  13Q GAIN WILD-TYPE 19   1   2   1   1  4
D17V5, multiclass
D17V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       0        1        2        0         1
  13Q GAIN WILD-TYPE           1       3        3        4        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED           2         2         1          1          2
  13Q GAIN WILD-TYPE         2         0         0          0          4
                    vv
clus                 STAGE IIIC STAGE IV
  13Q GAIN MUTATED            2        0
  13Q GAIN WILD-TYPE          4        1
D17V7, multiclass

Clustering(18) Variable = 14q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    0  1
  14Q GAIN WILD-TYPE  9 12
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 21 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 12 
$`14Q GAIN MUTATED`
TCGA-EE-A29L 
        1.08 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               2.43 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08              48.79 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               9.99 
[1] "1.1 - 1.1 (1.1)"   "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"14Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 21 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19D 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
D18V2, continuous
                    vv
clus                 DISTANT METASTASIS
  14Q GAIN MUTATED                    1
  14Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q GAIN MUTATED                                                                                          1
  14Q GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                     2
  14Q GAIN WILD-TYPE                  26
D18V3, multiclass
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      26
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    3
  14Q GAIN WILD-TYPE   15   26
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  14Q GAIN MUTATED    3   0   0   0   0  1
  14Q GAIN WILD-TYPE 24   3   4   1   2  4
D18V5, multiclass
D18V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q GAIN MUTATED             0       0        0        0        1         0
  14Q GAIN WILD-TYPE           1       3        4        6        3         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED           1         1         0          0          0
  14Q GAIN WILD-TYPE         3         1         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  14Q GAIN MUTATED            1        0
  14Q GAIN WILD-TYPE          5        1
D18V7, multiclass

Clustering(19) Variable = 15q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  0
  15Q GAIN WILD-TYPE  7 13
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                 13 
$`15Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A2A1 
        5.39        25.28 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        2.43         8.09        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.39               1.08 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             25.28              48.79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            15.335              9.830 
[1] "5.4 - 25.3 (15.3)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"15Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1I1         TCGA-DA-A3F3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A2 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS
  15Q GAIN MUTATED                    2
  15Q GAIN WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          2
  15Q GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                     2
  15Q GAIN WILD-TYPE                  26
D19V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      26
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    3
  15Q GAIN WILD-TYPE   13   26
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  15Q GAIN MUTATED    4   0   0   1   0  0
  15Q GAIN WILD-TYPE 23   3   4   0   2  5
D19V5, multiclass
D19V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q GAIN MUTATED             0       1        0        1        0         0
  15Q GAIN WILD-TYPE           1       2        4        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED           1         1         0          0          1
  15Q GAIN WILD-TYPE         3         1         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  15Q GAIN MUTATED            0        0
  15Q GAIN WILD-TYPE          6        1
D19V7, multiclass

Clustering(20) Variable = 16p gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  2
  16P GAIN WILD-TYPE  8 11
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 19 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 11 
$`16P GAIN MUTATED`
TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D 
        8.84         9.67         3.52 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S 
        7.00        11.57         4.27         1.08         8.12         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19N TCGA-GN-A267 
        2.43         8.09        25.28        23.90        42.84        16.21 
TCGA-GN-A268 
       15.39 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.52               1.08 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              9.67              48.79 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.84              11.57 
[1] "3.5 - 9.7 (8.8)"   "1.1 - 48.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS
  16P GAIN MUTATED                    1
  16P GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P GAIN MUTATED                                                                                          4
  16P GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                     1
  16P GAIN WILD-TYPE                  27
D20V3, multiclass
                                                                                          clus
vv                                                                                         16P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      27
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3    3
  16P GAIN WILD-TYPE   13   26
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  16P GAIN MUTATED    5   0   1   0   0  0
  16P GAIN WILD-TYPE 22   3   3   1   2  5
D20V5, multiclass
D20V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P GAIN MUTATED             0       0        0        2        0         1
  16P GAIN WILD-TYPE           1       3        4        4        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED           1         1         0          0          0
  16P GAIN WILD-TYPE         3         1         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  16P GAIN MUTATED            1        0
  16P GAIN WILD-TYPE          5        1
D20V7, multiclass

Clustering(21) Variable = 16q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  1
  16Q GAIN WILD-TYPE  8 12
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 20 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 12 
$`16Q GAIN MUTATED`
TCGA-EE-A29R TCGA-ER-A19D 
        8.84         3.52 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S 
        7.00        11.57         4.27         1.08         8.12         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N 
        2.43         8.09        25.28        23.90         9.67        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.52               1.08 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.84              48.79 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.18              10.78 
[1] "3.5 - 8.8 (6.2)"   "1.1 - 48.8 (10.8)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"16Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29S 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D21V2, continuous
                    vv
clus                 DISTANT METASTASIS
  16Q GAIN MUTATED                    1
  16Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q GAIN MUTATED                                                                                          3
  16Q GAIN WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                     1
  16Q GAIN WILD-TYPE                  27
D21V3, multiclass
                                                                                          clus
vv                                                                                         16Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      27
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3    2
  16Q GAIN WILD-TYPE   13   27
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  16Q GAIN MUTATED    4   0   1   0   0  0
  16Q GAIN WILD-TYPE 23   3   3   1   2  5
D21V5, multiclass
D21V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q GAIN MUTATED             0       0        0        1        0         1
  16Q GAIN WILD-TYPE           1       3        4        5        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED           1         1         0          0          0
  16Q GAIN WILD-TYPE         3         1         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  16Q GAIN MUTATED            1        0
  16Q GAIN WILD-TYPE          5        1
D21V7, multiclass

Clustering(22) Variable = 17p gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    1  1
  17P GAIN WILD-TYPE  8 12
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 20 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 12 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV 
       16.47         5.39 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5.39               1.08 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             16.47              48.79 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             10.93               9.83 
[1] "5.4 - 16.5 (10.9)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"17P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q8         TCGA-D3-A2J8         TCGA-DA-A1HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A3F3         TCGA-EE-A17X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A29L         TCGA-EE-A29Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29R         TCGA-EE-A29S         TCGA-EE-A29V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A1         TCGA-EE-A2A2 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
D22V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17P GAIN MUTATED                    0
  17P GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P GAIN MUTATED                                                                                          2
  17P GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                     1
  17P GAIN WILD-TYPE                  27
D22V3, multiclass
                                                                                          clus
vv                                                                                         17P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      27
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    0
  17P GAIN WILD-TYPE   13   29
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  0                 29
                    vv
clus                 N0 N1A N1B N2A N2B N3
  17P GAIN MUTATED    1   0   0   1   0  1
  17P GAIN WILD-TYPE 26   3   4   0   2  4
D22V5, multiclass
D22V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P GAIN MUTATED             0       0        0        0        0         0
  17P GAIN WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED           0         1         0          0          1
  17P GAIN WILD-TYPE         4         1         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  17P GAIN MUTATED            1        0
  17P GAIN WILD-TYPE          5        1
D22V7, multiclass

Clustering(23) Variable = 17q gain mutation analysis
D23V1, survival
                    sevent
clus2                0 1
  17Q GAIN MUTATED   1 4
  17Q GAIN WILD-TYPE 8 9
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 17 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                  9 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-EE-A185 TCGA-EE-A29L TCGA-GN-A268 
       16.47         5.39         4.27         1.08        15.39 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.12         8.84         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       23.90         9.67         3.52        42.84        16.21 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.08               2.43 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             16.47              48.79 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.39               9.99 
[1] "1.1 - 16.5 (5.4)"  "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
  "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
  "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
  "17Q GAIN MUTATED" 
[1] "hr=" "2.4"
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17Q GAIN MUTATED                    0
  17Q GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          2
  17Q GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                     5
  17Q GAIN WILD-TYPE                  23
D23V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      23
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    2
  17Q GAIN WILD-TYPE   11   27
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                5                 11
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  17Q GAIN MUTATED    2   0   0   1   0  3
  17Q GAIN WILD-TYPE 25   3   4   0   2  2
D23V5, multiclass
D23V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        0        0        0         0
  17Q GAIN WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED           1         1         0          0          1
  17Q GAIN WILD-TYPE         3         1         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  17Q GAIN MUTATED            3        0
  17Q GAIN WILD-TYPE          3        1
D23V7, multiclass

Clustering(24) Variable = 18p gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    1  2
  18P GAIN WILD-TYPE  8 11
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 19 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 11 
$`18P GAIN MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29L TCGA-GN-A267 
       39.19         1.08        16.21 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A268 
       15.39 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.08               2.43 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             39.19              48.79 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             16.21               9.67 
[1] "1.1 - 39.2 (16.2)" "2.4 - 48.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268 
"18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268 
"18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A268 
"18P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18P GAIN MUTATED                    0
  18P GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          2
  18P GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                     2
  18P GAIN WILD-TYPE                  26
D24V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      26
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    3
  18P GAIN WILD-TYPE   15   26
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  18P GAIN MUTATED    1   1   0   0   0  2
  18P GAIN WILD-TYPE 26   2   4   1   2  3
D24V5, multiclass
D24V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P GAIN MUTATED             0       0        0        0        0         0
  18P GAIN WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED           0         1         0          1          0
  18P GAIN WILD-TYPE         4         1         1          0          6
                    vv
clus                 STAGE IIIC STAGE IV
  18P GAIN MUTATED            2        0
  18P GAIN WILD-TYPE          4        1
D24V7, multiclass

Clustering(25) Variable = 18q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    1  2
  18Q GAIN WILD-TYPE  8 11
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 19 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 11 
$`18Q GAIN MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29L TCGA-GN-A267 
       39.19         1.08        16.21 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A268 
       15.39 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               2.43 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             39.19              48.79 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             16.21               9.67 
[1] "1.1 - 39.2 (16.2)" "2.4 - 48.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268 
"18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268 
"18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A268 
"18Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D25V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18Q GAIN MUTATED                    0
  18Q GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          2
  18Q GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     2
  18Q GAIN WILD-TYPE                  26
D25V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      26
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE   15   26
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  18Q GAIN MUTATED    1   1   0   0   0  2
  18Q GAIN WILD-TYPE 26   2   4   1   2  3
D25V5, multiclass
D25V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q GAIN MUTATED             0       0        0        0        0         0
  18Q GAIN WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED           0         1         0          1          0
  18Q GAIN WILD-TYPE         4         1         1          0          6
                    vv
clus                 STAGE IIIC STAGE IV
  18Q GAIN MUTATED            2        0
  18Q GAIN WILD-TYPE          4        1
D25V7, multiclass

Clustering(26) Variable = 19p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    1  1
  19P GAIN WILD-TYPE  8 12
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 20 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 12 
$`19P GAIN MUTATED`
TCGA-EE-A29L TCGA-EE-A29R 
        1.08         8.84 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
        7.00        11.57         4.27         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.08               2.43 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              8.84              48.79 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              4.96              10.78 
[1] "1.1 - 8.8 (5.0)"   "2.4 - 48.8 (10.8)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29S         TCGA-EE-A29V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A1         TCGA-EE-A2A2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A5         TCGA-ER-A19D         TCGA-ER-A19N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
D26V2, continuous
                    vv
clus                 DISTANT METASTASIS
  19P GAIN MUTATED                    2
  19P GAIN WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P GAIN MUTATED                                                                                          0
  19P GAIN WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                     3
  19P GAIN WILD-TYPE                  25
D26V3, multiclass
                                                                                          clus
vv                                                                                         19P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      25
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    2
  19P GAIN WILD-TYPE   13   27
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                 13
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  19P GAIN MUTATED    2   0   1   0   0  1
  19P GAIN WILD-TYPE 25   3   3   1   2  4
D26V5, multiclass
D26V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P GAIN MUTATED             0       1        0        0        0         0
  19P GAIN WILD-TYPE           1       2        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED           1         0         0          0          0
  19P GAIN WILD-TYPE         3         2         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  19P GAIN MUTATED            2        0
  19P GAIN WILD-TYPE          4        1
D26V7, multiclass

Clustering(27) Variable = 19q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE  8 11
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 19 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 11 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-EE-A29L TCGA-EE-A29R 
       16.47         1.08         8.84 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       28.08         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         8.12         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.08               2.43 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             16.47              48.79 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              8.84               9.99 
[1] "1.1 - 16.5 (8.8)"  "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS
  19Q GAIN MUTATED                    2
  19Q GAIN WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q GAIN MUTATED                                                                                          1
  19Q GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                     3
  19Q GAIN WILD-TYPE                  25
D27V3, multiclass
                                                                                          clus
vv                                                                                         19Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      25
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      4    2
  19Q GAIN WILD-TYPE   12   27
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                4                 12
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  19Q GAIN MUTATED    2   0   1   0   0  2
  19Q GAIN WILD-TYPE 25   3   3   1   2  3
D27V5, multiclass
D27V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q GAIN MUTATED             0       0        0        0        0         0
  19Q GAIN WILD-TYPE           1       3        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED           2         0         0          0          0
  19Q GAIN WILD-TYPE         2         2         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3        0
  19Q GAIN WILD-TYPE          3        1
D27V7, multiclass

Clustering(28) Variable = 20p gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    3  2
  20P GAIN WILD-TYPE  6 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 17 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 11 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 
       16.47         5.39         8.84        25.28         9.67 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         1.08         8.12         9.99         2.43         8.09 
TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         3.52        42.84        16.21        15.39 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5.39               1.08 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             25.28              48.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              9.67               9.99 
[1] "5.4 - 25.3 (9.7)"  "1.1 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20P GAIN MUTATED                    1
  20P GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                          5
  20P GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                     4
  20P GAIN WILD-TYPE                  24
D28V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      24
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5    5
  20P GAIN WILD-TYPE   11   24
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 11
  MALE                  5                 24
                    vv
clus                 N0 N1A N1B N2A N2B N3
  20P GAIN MUTATED    6   1   1   1   0  1
  20P GAIN WILD-TYPE 21   2   3   0   2  4
D28V5, multiclass
D28V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             0       0        1        2        0         1
  20P GAIN WILD-TYPE           1       3        3        4        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED           1         1         0          0          2
  20P GAIN WILD-TYPE         3         1         1          1          4
                    vv
clus                 STAGE IIIC STAGE IV
  20P GAIN MUTATED            2        0
  20P GAIN WILD-TYPE          4        1
D28V7, multiclass

Clustering(29) Variable = 20q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    4  3
  20Q GAIN WILD-TYPE  5 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 7                 15 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 10 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A1 
       16.47         5.39        48.79         1.08         8.84        25.28 
TCGA-EE-A2A5 
        9.67 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38        39.19         7.00        11.57         4.27 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-ER-A19D 
        8.12         9.99         2.43         8.09        23.90         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.08               2.43 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             48.79              42.84 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              9.67               9.99 
[1] "1.1 - 48.8 (9.7)"  "2.4 - 42.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"20Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20Q GAIN MUTATED                    1
  20Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                          5
  20Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                     7
  20Q GAIN WILD-TYPE                  21
D29V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      21
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    7
  20Q GAIN WILD-TYPE   10   22
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 10
  MALE                  7                 22
                    vv
clus                 N0 N1A N1B N2A N2B N3
  20Q GAIN MUTATED    6   1   1   1   1  2
  20Q GAIN WILD-TYPE 21   2   3   0   1  3
D29V5, multiclass
D29V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             0       0        1        2        0         1
  20Q GAIN WILD-TYPE           1       3        3        4        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED           1         1         0          0          3
  20Q GAIN WILD-TYPE         3         1         1          1          3
                    vv
clus                 STAGE IIIC STAGE IV
  20Q GAIN MUTATED            3        0
  20Q GAIN WILD-TYPE          3        1
D29V7, multiclass

Clustering(30) Variable = 21q gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    3  2
  21Q GAIN WILD-TYPE  6 11
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 17 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 11 
$`21Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        5.39         8.84        25.28         9.67         3.52 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
        8.09        23.90        42.84        16.21        15.39 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              3.52               1.08 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.28              48.79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              8.84              11.57 
[1] "3.5 - 25.3 (8.8)"  "1.1 - 48.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A268 
"21Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS
  21Q GAIN MUTATED                    0
  21Q GAIN WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          5
  21Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                     2
  21Q GAIN WILD-TYPE                  26
D30V3, multiclass
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      26
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    3
  21Q GAIN WILD-TYPE   12   26
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                 12
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  21Q GAIN MUTATED    5   0   1   1   0  0
  21Q GAIN WILD-TYPE 22   3   3   0   2  5
D30V5, multiclass
D30V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q GAIN MUTATED             0       0        0        3        0         1
  21Q GAIN WILD-TYPE           1       3        4        3        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED           0         1         0          0          1
  21Q GAIN WILD-TYPE         4         1         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  21Q GAIN MUTATED            1        0
  21Q GAIN WILD-TYPE          5        1
D30V7, multiclass

Clustering(31) Variable = 22q gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  3
  22Q GAIN WILD-TYPE  5 10
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 15 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 10 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29R 
       16.47         5.39        48.79        39.19         1.08         8.84 
TCGA-GN-A267 
       16.21 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q 
       28.08         8.38         7.00        11.57         4.27         8.12 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         2.43         8.09        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
        3.52        42.84        15.39 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.08               2.43 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             48.79              42.84 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             16.21               9.67 
[1] "1.1 - 48.8 (16.2)" "2.4 - 42.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268 
"22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268 
"22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A268 
"22Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS
  22Q GAIN MUTATED                    1
  22Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                          4
  22Q GAIN WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                     5
  22Q GAIN WILD-TYPE                  23
D31V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      23
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5    5
  22Q GAIN WILD-TYPE   11   24
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                5                 11
  MALE                  5                 24
                    vv
clus                 N0 N1A N1B N2A N2B N3
  22Q GAIN MUTATED    2   1   2   1   1  3
  22Q GAIN WILD-TYPE 25   2   2   0   1  2
D31V5, multiclass
D31V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q GAIN MUTATED             0       0        0        0        0         1
  22Q GAIN WILD-TYPE           1       3        4        6        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED           0         1         1          1          2
  22Q GAIN WILD-TYPE         4         1         0          0          4
                    vv
clus                 STAGE IIIC STAGE IV
  22Q GAIN MUTATED            4        0
  22Q GAIN WILD-TYPE          2        1
D31V7, multiclass

Clustering(32) Variable = 4p loss mutation analysis
D32V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    0  2
  4P LOSS WILD-TYPE  9 11
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                11 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-ER-A19D 
       16.47         3.52 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       28.08         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N 
        2.43         8.09        25.28        23.90         9.67        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3.52              1.08 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            16.47             48.79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            9.995             9.830 
[1] "3.5 - 16.5 (10.0)" "1.1 - 48.8 (9.8)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                20 
       TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X        TCGA-EE-A185 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-ER-A19N        TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D32V2, continuous
                   vv
clus                DISTANT METASTASIS
  4P LOSS MUTATED                    1
  4P LOSS WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          2
  4P LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     2
  4P LOSS WILD-TYPE                  26
D32V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     26
D32V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5    0
  4P LOSS WILD-TYPE   11   29
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               5                11
  MALE                 0                29
                   vv
clus                N0 N1A N1B N2A N2B N3
  4P LOSS MUTATED    4   0   0   0   0  1
  4P LOSS WILD-TYPE 23   3   4   1   2  4
D32V5, multiclass
D32V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             0       1        1        1        0         0
  4P LOSS WILD-TYPE           1       2        3        5        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P LOSS MUTATED           0         1         0          0          0
  4P LOSS WILD-TYPE         4         1         1          1          6
                   vv
clus                STAGE IIIC STAGE IV
  4P LOSS MUTATED            1        0
  4P LOSS WILD-TYPE          5        1
D32V7, multiclass

Clustering(33) Variable = 4q loss mutation analysis
D33V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    0  3
  4Q LOSS WILD-TYPE  9 10
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                19 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                10 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-ER-A19D 
       16.47        28.08         3.52 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
        8.38         5.39        48.79        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28        23.90         9.67        42.84        16.21 
TCGA-GN-A268 
       15.39 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3.52              1.08 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            28.08             48.79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            16.47              9.67 
[1] "3.5 - 28.1 (16.5)" "1.1 - 48.8 (9.7)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "4Q LOSS MUTATED"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D33V2, continuous
                   vv
clus                DISTANT METASTASIS
  4Q LOSS MUTATED                    1
  4Q LOSS WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q LOSS MUTATED                                                                                          2
  4Q LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                     3
  4Q LOSS WILD-TYPE                  25
D33V3, multiclass
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     25
D33V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5    1
  4Q LOSS WILD-TYPE   11   28
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               5                11
  MALE                 1                28
                   vv
clus                N0 N1A N1B N2A N2B N3
  4Q LOSS MUTATED    4   0   0   0   0  2
  4Q LOSS WILD-TYPE 23   3   4   1   2  3
D33V5, multiclass
D33V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       1        1        1        0         0
  4Q LOSS WILD-TYPE           1       2        3        5        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED           0         1         0          0          0
  4Q LOSS WILD-TYPE         4         1         1          1          6
                   vv
clus                STAGE IIIC STAGE IV
  4Q LOSS MUTATED            1        1
  4Q LOSS WILD-TYPE          5        0
D33V7, multiclass

Clustering(34) Variable = 5p loss mutation analysis
D34V1, survival
                   sevent
clus2               0 1
  5P LOSS MUTATED   2 4
  5P LOSS WILD-TYPE 7 9
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                16 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                 9 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A2A2 TCGA-GN-A268 
       16.47        48.79        11.57         4.27        23.90        15.39 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A29L 
       28.08         8.38         5.39        39.19         7.00         1.08 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.12         8.84         9.99         2.43         8.09        25.28 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        9.67         3.52        42.84        16.21 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             4.27              1.08 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            48.79             42.84 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            15.93              8.61 
[1] "4.3 - 48.8 (15.9)" "1.1 - 42.8 (8.6)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
[1] "hr=" "1.2"
D34V2, continuous
                   vv
clus                DISTANT METASTASIS
  5P LOSS MUTATED                    2
  5P LOSS WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          0
  5P LOSS WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                     8
  5P LOSS WILD-TYPE                  20
D34V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     20
D34V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    5
  5P LOSS WILD-TYPE   11   24
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                11
  MALE                 5                24
                   vv
clus                N0 N1A N1B N2A N2B N3
  5P LOSS MUTATED    5   0   2   0   1  2
  5P LOSS WILD-TYPE 22   3   2   1   1  3
D34V5, multiclass
D34V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       1        2        0        0         0
  5P LOSS WILD-TYPE           1       2        2        6        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P LOSS MUTATED           2         0         1          0          2
  5P LOSS WILD-TYPE         2         2         0          1          4
                   vv
clus                STAGE IIIC STAGE IV
  5P LOSS MUTATED            2        0
  5P LOSS WILD-TYPE          4        1
D34V7, multiclass

Clustering(35) Variable = 5q loss mutation analysis
D35V1, survival
                   sevent
clus2               0 1
  5Q LOSS MUTATED   2 5
  5Q LOSS WILD-TYPE 7 8
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                15 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                 8 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A2 
       28.08        48.79        11.57         4.27         2.43        23.90 
TCGA-GN-A268 
       15.39 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A29L 
       16.47         8.38         5.39        39.19         7.00         1.08 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 
        8.12         8.84         9.99         8.09        25.28         9.67 
TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        3.52        42.84        16.21 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.43              1.08 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            48.79             42.84 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            15.39              8.84 
[1] "2.4 - 48.8 (15.4)" "1.1 - 42.8 (8.8)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
[1] "hr=" "1"  
D35V2, continuous
                   vv
clus                DISTANT METASTASIS
  5Q LOSS MUTATED                    4
  5Q LOSS WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          0
  5Q LOSS WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                     8
  5Q LOSS WILD-TYPE                  20
D35V3, multiclass
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     20
D35V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      4    8
  5Q LOSS WILD-TYPE   12   21
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               4                12
  MALE                 8                21
                   vv
clus                N0 N1A N1B N2A N2B N3
  5Q LOSS MUTATED    6   0   3   0   1  2
  5Q LOSS WILD-TYPE 21   3   1   1   1  3
D35V5, multiclass
D35V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             1       1        2        0        1         0
  5Q LOSS WILD-TYPE           0       2        2        6        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED           1         0         1          0          2
  5Q LOSS WILD-TYPE         3         2         0          1          4
                   vv
clus                STAGE IIIC STAGE IV
  5Q LOSS MUTATED            2        1
  5Q LOSS WILD-TYPE          4        0
D35V7, multiclass

Clustering(36) Variable = 6p loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    2  1
  6P LOSS WILD-TYPE  7 12
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                19 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                1                12 
$`6P LOSS MUTATED`
TCGA-EE-A29Q TCGA-EE-A29X TCGA-EE-A2A1 
        8.12         8.09        25.28 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         4.27         1.08         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        2.43        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.09              1.08 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            25.28             48.79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.12              9.99 
[1] "8.1 - 25.3 (8.1)"  "1.1 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D36V2, continuous
                   vv
clus                DISTANT METASTASIS
  6P LOSS MUTATED                    3
  6P LOSS WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P LOSS MUTATED                                                                                          1
  6P LOSS WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                     2
  6P LOSS WILD-TYPE                  26
D36V3, multiclass
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     26
D36V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2    4
  6P LOSS WILD-TYPE   14   25
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               2                14
  MALE                 4                25
                   vv
clus                N0 N1A N1B N2A N2B N3
  6P LOSS MUTATED    5   0   1   0   0  0
  6P LOSS WILD-TYPE 22   3   3   1   2  5
D36V5, multiclass
D36V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             1       0        0        2        1         0
  6P LOSS WILD-TYPE           0       3        4        4        3         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P LOSS MUTATED           1         0         1          0          0
  6P LOSS WILD-TYPE         3         2         0          1          6
                   vv
clus                STAGE IIIC STAGE IV
  6P LOSS MUTATED            0        0
  6P LOSS WILD-TYPE          6        1
D36V7, multiclass

Clustering(37) Variable = 6q loss mutation analysis
D37V1, survival
                   sevent
clus2               0 1
  6Q LOSS MUTATED   6 8
  6Q LOSS WILD-TYPE 3 5
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               14                 8 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                 5 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       16.47        48.79         4.27         8.12         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N 
        8.09        25.28        23.90         9.67         3.52        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A29L TCGA-EE-A29R 
        1.08         8.84 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2.43              1.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            48.79             39.19 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            12.69              8.61 
[1] "2.4 - 48.8 (12.7)" "1.1 - 39.2 (8.6)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
[1] "hr=" "1.3"
D37V2, continuous
                   vv
clus                DISTANT METASTASIS
  6Q LOSS MUTATED                    5
  6Q LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                          4
  6Q LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    13
  6Q LOSS WILD-TYPE                  15
D37V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     15
D37V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     10   12
  6Q LOSS WILD-TYPE    6   17
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              10                 6
  MALE                12                17
                   vv
clus                N0 N1A N1B N2A N2B N3
  6Q LOSS MUTATED   12   2   3   0   1  2
  6Q LOSS WILD-TYPE 15   1   1   1   1  3
D37V5, multiclass
D37V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             1       0        2        4        1         1
  6Q LOSS WILD-TYPE           0       3        2        2        3         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q LOSS MUTATED           3         0         1          1          3
  6Q LOSS WILD-TYPE         1         2         0          0          3
                   vv
clus                STAGE IIIC STAGE IV
  6Q LOSS MUTATED            3        0
  6Q LOSS WILD-TYPE          3        1
D37V7, multiclass

Clustering(38) Variable = 8p loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    0  3
  8P LOSS WILD-TYPE  9 10
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                19 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                10 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-EE-A29V TCGA-EE-A2A5 
       16.47         2.43         9.67 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       28.08         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28        23.90         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             2.43              1.08 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            16.47             48.79 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             9.67              9.99 
[1] "2.4 - 16.5 (9.7)"  "1.1 - 48.8 (10.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D38V2, continuous
                   vv
clus                DISTANT METASTASIS
  8P LOSS MUTATED                    3
  8P LOSS WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P LOSS MUTATED                                                                                          1
  8P LOSS WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                     4
  8P LOSS WILD-TYPE                  24
D38V3, multiclass
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     24
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    5
  8P LOSS WILD-TYPE   13   24
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                13
  MALE                 5                24
                   vv
clus                N0 N1A N1B N2A N2B N3
  8P LOSS MUTATED    4   0   2   0   0  1
  8P LOSS WILD-TYPE 23   3   2   1   2  4
D38V5, multiclass
D38V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             0       2        1        1        0         0
  8P LOSS WILD-TYPE           1       1        3        5        4         3
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P LOSS MUTATED           0         0         1          0          0
  8P LOSS WILD-TYPE         4         2         0          1          6
                   vv
clus                STAGE IIIC STAGE IV
  8P LOSS MUTATED            2        0
  8P LOSS WILD-TYPE          4        1
D38V7, multiclass

Clustering(39) Variable = 9p loss mutation analysis
D39V1, survival
                   sevent
clus2               0 1
  9P LOSS MUTATED   5 9
  9P LOSS WILD-TYPE 4 4
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               14                 8 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                 4 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A17X TCGA-EE-A185 
       16.47        28.08        48.79        39.19        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 
        1.08         8.12         9.99         2.43         8.09         9.67 
TCGA-ER-A19N TCGA-GN-A268 
       42.84        15.39 

$`9P LOSS WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.38         5.39         7.00         8.84        25.28        23.90 
TCGA-ER-A19D TCGA-GN-A267 
        3.52        16.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.08              3.52 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            48.79             25.28 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.78              8.61 
[1] "1.1 - 48.8 (10.8)" "3.5 - 25.3 (8.6)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
[1] "hr=" "1"  
D39V2, continuous
                   vv
clus                DISTANT METASTASIS
  9P LOSS MUTATED                    5
  9P LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                          7
  9P LOSS WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                    16
  9P LOSS WILD-TYPE                  12
D39V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   16
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                     12
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10   18
  9P LOSS WILD-TYPE    6   11
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              10                 6
  MALE                18                11
                   vv
clus                N0 N1A N1B N2A N2B N3
  9P LOSS MUTATED   17   2   1   0   1  5
  9P LOSS WILD-TYPE 10   1   3   1   1  0
D39V5, multiclass
D39V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             1       1        2        3        3         2
  9P LOSS WILD-TYPE           0       2        2        3        1         1
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P LOSS MUTATED           4         1         0          0          3
  9P LOSS WILD-TYPE         0         1         1          1          3
                   vv
clus                STAGE IIIC STAGE IV
  9P LOSS MUTATED            5        1
  9P LOSS WILD-TYPE          1        0
D39V7, multiclass

Clustering(40) Variable = 9q loss mutation analysis
D40V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   6 5
  9Q LOSS WILD-TYPE 3 8
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                11 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                 8 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29Q 
       16.47        28.08        48.79        39.19         1.08         8.12 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-ER-A19N TCGA-GN-A268 
        9.99         8.09        23.90        42.84        15.39 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29R 
        8.38         5.39         7.00        11.57         4.27         8.84 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
        2.43        25.28         9.67         3.52        16.21 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1.08              2.43 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            48.79             25.28 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            16.47              8.38 
[1] "1.1 - 48.8 (16.5)" "2.4 - 25.3 (8.4)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q8        TCGA-D3-A2J8        TCGA-D3-A3MV 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1I1        TCGA-DA-A3F3        TCGA-EE-A17X 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A185        TCGA-EE-A29L        TCGA-EE-A29Q        TCGA-EE-A29R 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-ER-A19D        TCGA-ER-A19N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
[1] "hr=" "3.7"
D40V2, continuous
                   vv
clus                DISTANT METASTASIS
  9Q LOSS MUTATED                    4
  9Q LOSS WILD-TYPE                  4
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                          5
  9Q LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    13
  9Q LOSS WILD-TYPE                  15
D40V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     15
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   14
  9Q LOSS WILD-TYPE    8   15
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               8                 8
  MALE                14                15
                   vv
clus                N0 N1A N1B N2A N2B N3
  9Q LOSS MUTATED   12   2   1   0   1  4
  9Q LOSS WILD-TYPE 15   1   3   1   1  1
D40V5, multiclass
D40V6, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             1       0        1        2        2         1
  9Q LOSS WILD-TYPE           0       3        3        4        2         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q LOSS MUTATED           4         1         0          0          4
  9Q LOSS WILD-TYPE         0         1         1          1          2
                   vv
clus                STAGE IIIC STAGE IV
  9Q LOSS MUTATED            3        1
  9Q LOSS WILD-TYPE          3        0
D40V7, multiclass

Clustering(41) Variable = 10p loss mutation analysis
D41V1, survival
                    sevent
clus2                0 1
  10P LOSS MUTATED   1 9
  10P LOSS WILD-TYPE 8 4
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                10                 12 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 9                  4 
$`10P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1I1 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29X 
       16.47        28.08        39.19         4.27         1.08         8.09 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 TCGA-GN-A268 
        9.67         3.52        16.21        15.39 

$`10P LOSS WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29Q 
        8.38         5.39        48.79         7.00        11.57         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19N 
        8.84         9.99         2.43        25.28        23.90        42.84 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               2.43 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             39.19              48.79 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.530              9.415 
[1] "1.1 - 39.2 (12.5)" "2.4 - 48.8 (9.4)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268 
  "10P LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268 
  "10P LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A268 
  "10P LOSS MUTATED" 
[1] "hr=" "2.6"
D41V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10P LOSS MUTATED                    3
  10P LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                          6
  10P LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    10
  10P LOSS WILD-TYPE                  18
D41V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      18
D41V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9   10
  10P LOSS WILD-TYPE    7   19
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                9                  7
  MALE                 10                 19
                    vv
clus                 N0 N1A N1B N2A N2B N3
  10P LOSS MUTATED   11   2   0   0   0  5
  10P LOSS WILD-TYPE 16   1   4   1   2  0
D41V5, multiclass
D41V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             1       1        2        3        0         1
  10P LOSS WILD-TYPE           0       2        2        3        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED           2         1         0          1          1
  10P LOSS WILD-TYPE         2         1         1          0          5
                    vv
clus                 STAGE IIIC STAGE IV
  10P LOSS MUTATED            4        1
  10P LOSS WILD-TYPE          2        0
D41V7, multiclass

Clustering(42) Variable = 10q loss mutation analysis
D42V1, survival
                    sevent
clus2                0 1
  10Q LOSS MUTATED   1 8
  10Q LOSS WILD-TYPE 8 5
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                  5 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-DA-A1I1 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29X 
       16.47        28.08        39.19         4.27         1.08         8.09 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
        9.67         3.52        16.21 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29Q 
        8.38         5.39        48.79         7.00        11.57         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19N 
        8.84         9.99         2.43        25.28        23.90        42.84 
TCGA-GN-A268 
       15.39 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.08               2.43 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             39.19              48.79 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              9.67               9.99 
[1] "1.1 - 39.2 (9.7)"  "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268 
"10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268 
"10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A268 
"10Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D42V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10Q LOSS MUTATED                    3
  10Q LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                          7
  10Q LOSS WILD-TYPE                                                                                        2
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                    10
  10Q LOSS WILD-TYPE                  18
D42V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  2
  REGIONAL LYMPH NODE                                                                                      18
D42V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9   11
  10Q LOSS WILD-TYPE    7   18
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                9                  7
  MALE                 11                 18
                    vv
clus                 N0 N1A N1B N2A N2B N3
  10Q LOSS MUTATED   12   2   0   0   0  5
  10Q LOSS WILD-TYPE 15   1   4   1   2  0
D42V5, multiclass
D42V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             1       1        2        3        1         1
  10Q LOSS WILD-TYPE           0       2        2        3        3         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED           2         1         0          1          1
  10Q LOSS WILD-TYPE         2         1         1          0          5
                    vv
clus                 STAGE IIIC STAGE IV
  10Q LOSS MUTATED            4        1
  10Q LOSS WILD-TYPE          2        0
D42V7, multiclass

Clustering(43) Variable = 11p loss mutation analysis
D43V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   5 7
  11P LOSS WILD-TYPE 4 6
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                12                 10 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                  6 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
       16.47        48.79        39.19         1.08         8.12         8.84 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
        2.43         8.09        23.90         9.67         3.52        16.21 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38         5.39         7.00        11.57         4.27 
TCGA-EE-A29S TCGA-EE-A2A1 TCGA-ER-A19N TCGA-GN-A268 
        9.99        25.28        42.84        15.39 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.08               4.27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.79              42.84 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             9.255             10.780 
[1] "1.1 - 48.8 (9.3)"  "4.3 - 42.8 (10.8)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268 
"11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268 
"11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A268 
"11P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D43V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11P LOSS MUTATED                    2
  11P LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                          5
  11P LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                     8
  11P LOSS WILD-TYPE                  20
D43V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      20
D43V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    7
  11P LOSS WILD-TYPE    8   22
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                8                  8
  MALE                  7                 22
                    vv
clus                 N0 N1A N1B N2A N2B N3
  11P LOSS MUTATED    6   1   3   0   1  3
  11P LOSS WILD-TYPE 21   2   1   1   1  2
D43V5, multiclass
D43V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             0       1        0        3        0         0
  11P LOSS WILD-TYPE           1       2        4        3        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED           1         1         0          1          2
  11P LOSS WILD-TYPE         3         1         1          0          4
                    vv
clus                 STAGE IIIC STAGE IV
  11P LOSS MUTATED            5        0
  11P LOSS WILD-TYPE          1        1
D43V7, multiclass

Clustering(44) Variable = 11q loss mutation analysis
D44V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   5 5
  11Q LOSS WILD-TYPE 4 8
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                10                 12 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  8 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
       16.47        48.79        39.19         1.08         8.12         8.84 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-GN-A267 
       23.90         9.67         3.52        16.21 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38         5.39         7.00        11.57         4.27 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-ER-A19N TCGA-GN-A268 
        9.99         2.43         8.09        25.28        42.84        15.39 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.08               2.43 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             48.79              42.84 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            12.940              9.185 
[1] "1.1 - 48.8 (12.9)" "2.4 - 42.8 (9.2)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268 
"11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268 
"11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A268 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D44V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11Q LOSS MUTATED                    2
  11Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          5
  11Q LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                     9
  11Q LOSS WILD-TYPE                  19
D44V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      19
D44V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    9
  11Q LOSS WILD-TYPE    9   20
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                7                  9
  MALE                  9                 20
                    vv
clus                 N0 N1A N1B N2A N2B N3
  11Q LOSS MUTATED    8   1   2   0   1  3
  11Q LOSS WILD-TYPE 19   2   2   1   1  2
D44V5, multiclass
D44V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             0       2        0        2        1         0
  11Q LOSS WILD-TYPE           1       1        4        4        3         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED           1         2         0          1          2
  11Q LOSS WILD-TYPE         3         0         1          0          4
                    vv
clus                 STAGE IIIC STAGE IV
  11Q LOSS MUTATED            4        0
  11Q LOSS WILD-TYPE          2        1
D44V7, multiclass

Clustering(45) Variable = 12p loss mutation analysis
D45V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  1
  12P LOSS WILD-TYPE  5 12
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 17 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 12 
$`12P LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 TCGA-GN-A267 
       39.19         8.12         9.99        23.90        16.21 

$`12P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29X 
       11.57         4.27         1.08         8.84         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
       25.28         9.67         3.52        42.84        15.39 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              8.12               1.08 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             39.19              48.79 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             16.21               8.84 
[1] "8.1 - 39.2 (16.2)" "1.1 - 48.8 (8.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-GN-A268 
"12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-GN-A268 
"12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-GN-A268 
"12P LOSS WILD-TYPE" 
[1] "hr=" "4.9"
D45V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12P LOSS MUTATED                    1
  12P LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P LOSS MUTATED                                                                                          2
  12P LOSS WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                     3
  12P LOSS WILD-TYPE                  25
D45V3, multiclass
                                                                                          clus
vv                                                                                         12P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      25
D45V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    5
  12P LOSS WILD-TYPE   15   24
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  5                 24
                    vv
clus                 N0 N1A N1B N2A N2B N3
  12P LOSS MUTATED    3   1   1   0   0  1
  12P LOSS WILD-TYPE 24   2   3   1   2  4
D45V5, multiclass
D45V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P LOSS MUTATED             1       0        0        0        0         1
  12P LOSS WILD-TYPE           0       3        4        6        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED           1         0         0          1          1
  12P LOSS WILD-TYPE         3         2         1          0          5
                    vv
clus                 STAGE IIIC STAGE IV
  12P LOSS MUTATED            1        0
  12P LOSS WILD-TYPE          5        1
D45V7, multiclass

Clustering(46) Variable = 12q loss mutation analysis
D46V1, survival
                    sevent
clus2                0 1
  12Q LOSS MUTATED   4 4
  12Q LOSS WILD-TYPE 5 9
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                 14 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                  9 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1I1 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 
       16.47        39.19         8.12         9.99         8.09        23.90 
TCGA-EE-A2A5 TCGA-GN-A267 
        9.67        16.21 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        48.79         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A1 TCGA-ER-A19D 
        4.27         1.08         8.84         2.43        25.28         3.52 
TCGA-ER-A19N TCGA-GN-A268 
       42.84        15.39 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.09               1.08 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             39.19              48.79 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.10               8.61 
[1] "8.1 - 39.2 (13.1)" "1.1 - 48.8 (8.6)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-GN-A268 
"12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-GN-A268 
"12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-GN-A268 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D46V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12Q LOSS MUTATED                    1
  12Q LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          3
  12Q LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     5
  12Q LOSS WILD-TYPE                  23
D46V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      23
D46V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    6
  12Q LOSS WILD-TYPE   13   23
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                3                 13
  MALE                  6                 23
                    vv
clus                 N0 N1A N1B N2A N2B N3
  12Q LOSS MUTATED    5   1   1   0   0  2
  12Q LOSS WILD-TYPE 22   2   3   1   2  3
D46V5, multiclass
D46V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             1       0        0        2        0         1
  12Q LOSS WILD-TYPE           0       3        4        4        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED           1         0         0          1          1
  12Q LOSS WILD-TYPE         3         2         1          0          5
                    vv
clus                 STAGE IIIC STAGE IV
  12Q LOSS MUTATED            2        0
  12Q LOSS WILD-TYPE          4        1
D46V7, multiclass

Clustering(47) Variable = 13q loss mutation analysis
D47V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    2  1
  13Q LOSS WILD-TYPE  7 12
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 12 
$`13Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-DA-A1HV TCGA-EE-A29Q 
       28.08        48.79         8.12 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       16.47         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
        4.27         1.08         8.84         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              8.12               1.08 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             48.79              42.84 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             28.08               9.67 
[1] "8.1 - 48.8 (28.1)" "1.1 - 42.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"13Q LOSS WILD-TYPE" 
[1] "hr=" "3.3"
D47V2, continuous
                    vv
clus                 DISTANT METASTASIS
  13Q LOSS MUTATED                    0
  13Q LOSS WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          1
  13Q LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                     3
  13Q LOSS WILD-TYPE                  25
D47V3, 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                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      25
D47V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    2
  13Q LOSS WILD-TYPE   14   27
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  13Q LOSS MUTATED    2   0   0   0   1  1
  13Q LOSS WILD-TYPE 25   3   4   1   1  4
D47V5, multiclass
D47V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        1        0        0         0
  13Q LOSS WILD-TYPE           1       3        3        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED           1         0         0          0          1
  13Q LOSS WILD-TYPE         3         2         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  13Q LOSS MUTATED            0        1
  13Q LOSS WILD-TYPE          6        0
D47V7, multiclass

Clustering(48) Variable = 14q loss mutation analysis
D48V1, survival
                    sevent
clus2                0 1
  14Q LOSS MUTATED   2 5
  14Q LOSS WILD-TYPE 7 8
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 15 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 5                  8 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29X TCGA-EE-A2A5 TCGA-GN-A267 
       16.47        48.79        39.19         8.09         9.67        16.21 
TCGA-GN-A268 
       15.39 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 
       28.08         8.38         5.39         7.00        11.57         4.27 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 
        1.08         8.12         8.84         9.99         2.43        25.28 
TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N 
       23.90         3.52        42.84 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              8.09               1.08 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             48.79              42.84 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             16.21               8.38 
[1] "8.1 - 48.8 (16.2)" "1.1 - 42.8 (8.4)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268 
  "14Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268 
  "14Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-GN-A268 
  "14Q LOSS MUTATED" 
[1] "hr=" "1.2"
D48V2, continuous
                    vv
clus                 DISTANT METASTASIS
  14Q LOSS MUTATED                    2
  14Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                          3
  14Q LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                     7
  14Q LOSS WILD-TYPE                  21
D48V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      21
D48V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4    8
  14Q LOSS WILD-TYPE   12   21
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                4                 12
  MALE                  8                 21
                    vv
clus                 N0 N1A N1B N2A N2B N3
  14Q LOSS MUTATED    7   2   0   0   1  2
  14Q LOSS WILD-TYPE 20   1   4   1   1  3
D48V5, multiclass
D48V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             1       1        0        2        1         0
  14Q LOSS WILD-TYPE           0       2        4        4        3         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED           1         1         0          1          2
  14Q LOSS WILD-TYPE         3         1         1          0          4
                    vv
clus                 STAGE IIIC STAGE IV
  14Q LOSS MUTATED            2        0
  14Q LOSS WILD-TYPE          4        1
D48V7, multiclass

Clustering(49) Variable = 15q loss mutation analysis
D49V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    1  2
  15Q LOSS WILD-TYPE  8 11
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                 19 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 11 
$`15Q LOSS MUTATED`
TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A2A5 
       39.19         1.08         9.67 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        48.79         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.57         4.27         8.12         8.84         9.99         2.43 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        8.09        25.28        23.90         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.08               2.43 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             39.19              48.79 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              9.67               9.99 
[1] "1.1 - 39.2 (9.7)"  "2.4 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"15Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D49V2, continuous
                    vv
clus                 DISTANT METASTASIS
  15Q LOSS MUTATED                    1
  15Q LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q LOSS MUTATED                                                                                          2
  15Q LOSS WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                     1
  15Q LOSS WILD-TYPE                  27
D49V3, multiclass
                                                                                          clus
vv                                                                                         15Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      27
D49V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    3
  15Q LOSS WILD-TYPE   15   26
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  15Q LOSS MUTATED    2   0   0   0   0  2
  15Q LOSS WILD-TYPE 25   3   4   1   2  3
D49V5, multiclass
D49V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       0        1        1        0         0
  15Q LOSS WILD-TYPE           1       3        3        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED           0         0         0          0          0
  15Q LOSS WILD-TYPE         4         2         1          1          6
                    vv
clus                 STAGE IIIC STAGE IV
  15Q LOSS MUTATED            2        0
  15Q LOSS WILD-TYPE          4        1
D49V7, multiclass

Clustering(50) Variable = 16q loss mutation analysis
D50V1, survival
                    sevent
clus2                0 1
  16Q LOSS MUTATED   0 4
  16Q LOSS WILD-TYPE 9 9
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 18 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                  9 
$`16Q LOSS MUTATED`
TCGA-EE-A185 TCGA-EE-A29X TCGA-EE-A2A5 TCGA-GN-A267 
        4.27         8.09         9.67        16.21 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        7.00        11.57         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A268 
        2.43        25.28        23.90         3.52        42.84        15.39 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              4.27               1.08 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.21              48.79 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              8.88              10.78 
[1] "4.3 - 16.2 (8.9)"  "1.1 - 48.8 (10.8)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268 
"16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268 
"16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A268 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "3"  
D50V2, continuous
                    vv
clus                 DISTANT METASTASIS
  16Q LOSS MUTATED                    1
  16Q LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          2
  16Q LOSS WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                     5
  16Q LOSS WILD-TYPE                  23
D50V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      23
D50V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2    6
  16Q LOSS WILD-TYPE   14   23
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  6                 23
                    vv
clus                 N0 N1A N1B N2A N2B N3
  16Q LOSS MUTATED    5   2   0   0   0  1
  16Q LOSS WILD-TYPE 22   1   4   1   2  4
D50V5, multiclass
D50V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             0       0        0        2        3         0
  16Q LOSS WILD-TYPE           1       3        4        4        1         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED           0         0         0          1          1
  16Q LOSS WILD-TYPE         4         2         1          0          5
                    vv
clus                 STAGE IIIC STAGE IV
  16Q LOSS MUTATED            1        0
  16Q LOSS WILD-TYPE          5        1
D50V7, multiclass

Clustering(51) Variable = 17p loss mutation analysis
D51V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   4 5
  17P LOSS WILD-TYPE 5 8
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  8 
$`17P LOSS MUTATED`
TCGA-DA-A1HV TCGA-DA-A3F3 TCGA-EE-A185 TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X 
       48.79         7.00         4.27         9.99         2.43         8.09 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
       25.28        23.90         9.67 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-EE-A17X 
       16.47        28.08         8.38         5.39        39.19        11.57 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
        1.08         8.12         8.84         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2.43               1.08 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             48.79              42.84 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.67              11.57 
[1] "2.4 - 48.8 (9.7)"  "1.1 - 42.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D51V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17P LOSS MUTATED                    3
  17P LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          2
  17P LOSS WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    10
  17P LOSS WILD-TYPE                  18
D51V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      18
D51V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3   12
  17P LOSS WILD-TYPE   13   17
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                3                 13
  MALE                 12                 17
                    vv
clus                 N0 N1A N1B N2A N2B N3
  17P LOSS MUTATED    9   1   2   0   2  1
  17P LOSS WILD-TYPE 18   2   2   1   0  4
D51V5, multiclass
D51V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             1       1        1        3        1         1
  17P LOSS WILD-TYPE           0       2        3        3        3         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED           1         0         0          0          4
  17P LOSS WILD-TYPE         3         2         1          1          2
                    vv
clus                 STAGE IIIC STAGE IV
  17P LOSS MUTATED            2        0
  17P LOSS WILD-TYPE          4        1
D51V7, multiclass

Clustering(52) Variable = 17q loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    0  1
  17Q LOSS WILD-TYPE  9 12
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 21 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 12 
$`17Q LOSS MUTATED`
TCGA-EE-A29X 
        8.09 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43        25.28        23.90         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       42.84        16.21        15.39 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.09               1.08 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.09              48.79 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.09               9.99 
[1] "8.1 - 8.1 (8.1)"   "1.1 - 48.8 (10.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"17Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 21 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A2A1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
D52V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17Q LOSS MUTATED                    1
  17Q LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          1
  17Q LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                     1
  17Q LOSS WILD-TYPE                  27
D52V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      27
D52V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE   15   27
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  17Q LOSS MUTATED    2   1   0   0   0  0
  17Q LOSS WILD-TYPE 25   2   4   1   2  5
D52V5, multiclass
D52V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             1       0        0        1        0         0
  17Q LOSS WILD-TYPE           0       3        4        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED           0         0         0          0          1
  17Q LOSS WILD-TYPE         4         2         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  17Q LOSS MUTATED            0        0
  17Q LOSS WILD-TYPE          6        1
D52V7, multiclass

Clustering(53) Variable = 18p loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    1  3
  18P LOSS WILD-TYPE  8 10
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 18 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 10 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A29V TCGA-EE-A29X 
       16.47        48.79         2.43         8.09 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
        4.27         1.08         8.12         8.84         9.99        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.43               1.08 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             48.79              42.84 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             12.28               9.83 
[1] "2.4 - 48.8 (12.3)" "1.1 - 42.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D53V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18P LOSS MUTATED                    3
  18P LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          1
  18P LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                     5
  18P LOSS WILD-TYPE                  23
D53V3, multiclass
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      23
D53V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    5
  18P LOSS WILD-TYPE   12   24
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                4                 12
  MALE                  5                 24
                    vv
clus                 N0 N1A N1B N2A N2B N3
  18P LOSS MUTATED    4   2   1   0   1  1
  18P LOSS WILD-TYPE 23   1   3   1   1  4
D53V5, multiclass
D53V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             1       1        0        1        0         0
  18P LOSS WILD-TYPE           0       2        4        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED           1         0         0          0          3
  18P LOSS WILD-TYPE         3         2         1          1          3
                    vv
clus                 STAGE IIIC STAGE IV
  18P LOSS MUTATED            2        0
  18P LOSS WILD-TYPE          4        1
D53V7, multiclass

Clustering(54) Variable = 18q loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    1  3
  18Q LOSS WILD-TYPE  8 10
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 18 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 10 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A29V TCGA-EE-A29X 
       16.47        48.79         2.43         8.09 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 
        4.27         1.08         8.12         8.84         9.99        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 TCGA-GN-A268 
       23.90         9.67         3.52        42.84        16.21        15.39 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              2.43               1.08 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             48.79              42.84 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             12.28               9.83 
[1] "2.4 - 48.8 (12.3)" "1.1 - 42.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"18Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D54V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18Q LOSS MUTATED                    3
  18Q LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          1
  18Q LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                     4
  18Q LOSS WILD-TYPE                  24
D54V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      24
D54V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    5
  18Q LOSS WILD-TYPE   13   24
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                 13
  MALE                  5                 24
                    vv
clus                 N0 N1A N1B N2A N2B N3
  18Q LOSS MUTATED    3   2   1   0   1  1
  18Q LOSS WILD-TYPE 24   1   3   1   1  4
D54V5, multiclass
D54V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             1       0        0        1        0         0
  18Q LOSS WILD-TYPE           0       3        4        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED           1         0         0          0          3
  18Q LOSS WILD-TYPE         3         2         1          1          3
                    vv
clus                 STAGE IIIC STAGE IV
  18Q LOSS MUTATED            2        0
  18Q LOSS WILD-TYPE          4        1
D54V7, multiclass

Clustering(55) Variable = 19p loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    1  2
  19P LOSS WILD-TYPE  8 11
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 19 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 11 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A29X 
       16.47        48.79         8.09 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 TCGA-EE-A17X 
       28.08         8.38         5.39        39.19         7.00        11.57 
TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
        4.27         1.08         8.12         8.84         9.99         2.43 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              8.09               1.08 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.79              42.84 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.47               9.67 
[1] "8.1 - 48.8 (16.5)" "1.1 - 42.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D55V2, continuous
                    vv
clus                 DISTANT METASTASIS
  19P LOSS MUTATED                    1
  19P LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P LOSS MUTATED                                                                                          1
  19P LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                     4
  19P LOSS WILD-TYPE                  24
D55V3, multiclass
                                                                                          clus
vv                                                                                         19P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      24
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4    2
  19P LOSS WILD-TYPE   12   27
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 12
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  19P LOSS MUTATED    3   1   0   0   1  1
  19P LOSS WILD-TYPE 24   2   4   1   1  4
D55V5, multiclass
D55V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             1       0        0        1        0         0
  19P LOSS WILD-TYPE           0       3        4        5        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED           0         1         0          0          2
  19P LOSS WILD-TYPE         4         1         1          1          4
                    vv
clus                 STAGE IIIC STAGE IV
  19P LOSS MUTATED            1        0
  19P LOSS WILD-TYPE          5        1
D55V7, multiclass

Clustering(56) Variable = 19q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE  7 12
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 19 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 12 
$`19Q LOSS MUTATED`
TCGA-DA-A1HV TCGA-EE-A29S TCGA-EE-A29X 
       48.79         9.99         8.09 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47        28.08         8.38         5.39        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29V 
       11.57         4.27         1.08         8.12         8.84         2.43 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19N TCGA-GN-A267 
       25.28        23.90         9.67         3.52        42.84        16.21 
TCGA-GN-A268 
       15.39 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              8.09               1.08 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.79              42.84 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              9.99               9.67 
[1] "8.1 - 48.8 (10.0)" "1.1 - 42.8 (9.7)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"19Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D56V2, continuous
                    vv
clus                 DISTANT METASTASIS
  19Q LOSS MUTATED                    0
  19Q LOSS WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q LOSS MUTATED                                                                                          0
  19Q LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                     4
  19Q LOSS WILD-TYPE                  24
D56V3, multiclass
                                                                                          clus
vv                                                                                         19Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      24
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    2
  19Q LOSS WILD-TYPE   14   27
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  2                 27
                    vv
clus                 N0 N1A N1B N2A N2B N3
  19Q LOSS MUTATED    2   1   0   0   1  0
  19Q LOSS WILD-TYPE 25   2   4   1   1  5
D56V5, multiclass
D56V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q LOSS MUTATED             0       0        0        1        0         1
  19Q LOSS WILD-TYPE           1       3        4        5        4         2
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED           0         0         0          0          2
  19Q LOSS WILD-TYPE         4         2         1          1          4
                    vv
clus                 STAGE IIIC STAGE IV
  19Q LOSS MUTATED            0        0
  19Q LOSS WILD-TYPE          6        1
D56V7, multiclass

Clustering(57) Variable = 21q loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    1  1
  21Q LOSS WILD-TYPE  8 12
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 12 
$`21Q LOSS MUTATED`
TCGA-EE-A2A2 TCGA-GN-A268 
       23.90        15.39 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 
       16.47        28.08         8.38         5.39        48.79        39.19 
TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R 
        7.00        11.57         4.27         1.08         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D 
        9.99         2.43         8.09        25.28         9.67         3.52 
TCGA-ER-A19N TCGA-GN-A267 
       42.84        16.21 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             15.39               1.08 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             23.90              48.79 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            19.645              9.255 
[1] "15.4 - 23.9 (19.6)" "1.1 - 48.8 (9.3)"  
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
  "21Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
  "21Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
  "21Q LOSS MUTATED" 
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A5         TCGA-ER-A19D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-GN-A267 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D57V2, continuous
                    vv
clus                 DISTANT METASTASIS
  21Q LOSS MUTATED                    1
  21Q LOSS WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          0
  21Q LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                     3
  21Q LOSS WILD-TYPE                  25
D57V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      25
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    3
  21Q LOSS WILD-TYPE   15   26
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                1                 15
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  21Q LOSS MUTATED    3   0   1   0   0  0
  21Q LOSS WILD-TYPE 24   3   3   1   2  5
D57V5, multiclass
D57V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q LOSS MUTATED             0       1        0        0        0         0
  21Q LOSS WILD-TYPE           1       2        4        6        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED           1         1         0          0          1
  21Q LOSS WILD-TYPE         3         1         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  21Q LOSS MUTATED            0        0
  21Q LOSS WILD-TYPE          6        1
D57V7, multiclass

Clustering(58) Variable = 22q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    0  2
  22Q LOSS WILD-TYPE  9 11
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 20 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 11 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-ER-A19D 
       28.08         3.52 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F3 
       16.47         8.38         5.39        48.79        39.19         7.00 
TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       11.57         4.27         1.08         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19N 
        2.43         8.09        25.28        23.90         9.67        42.84 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              3.52               1.08 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             28.08              48.79 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             15.80               9.83 
[1] "3.5 - 28.1 (15.8)" "1.1 - 48.8 (9.8)" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q8         TCGA-D3-A2J8 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MV         TCGA-DA-A1HV         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F3         TCGA-EE-A17X         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29V         TCGA-EE-A29X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19N         TCGA-GN-A267 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A268 
"22Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-D3-A1Q1         TCGA-D3-A2J8         TCGA-D3-A3MV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HV         TCGA-DA-A1I1         TCGA-DA-A3F3 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A185         TCGA-EE-A29L 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29V         TCGA-EE-A29X         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
D58V2, continuous
                    vv
clus                 DISTANT METASTASIS
  22Q LOSS MUTATED                    0
  22Q LOSS WILD-TYPE                  8
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q LOSS MUTATED                                                                                          2
  22Q LOSS WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                     3
  22Q LOSS WILD-TYPE                  25
D58V3, multiclass
                                                                                          clus
vv                                                                                         22Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        8
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      25
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2    3
  22Q LOSS WILD-TYPE   14   26
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                2                 14
  MALE                  3                 26
                    vv
clus                 N0 N1A N1B N2A N2B N3
  22Q LOSS MUTATED    3   1   0   0   0  1
  22Q LOSS WILD-TYPE 24   2   4   1   2  4
D58V5, multiclass
D58V6, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       1        0        2        0         0
  22Q LOSS WILD-TYPE           1       2        4        4        4         3
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED           0         0         0          0          1
  22Q LOSS WILD-TYPE         4         2         1          1          5
                    vv
clus                 STAGE IIIC STAGE IV
  22Q LOSS MUTATED            0        1
  22Q LOSS WILD-TYPE          6        0
D58V7, 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")
