
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-NF1_Any_Mutants/3164407/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-NF1_Any_Mutants/3215659/SKCM-NF1_Any_Mutants.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-NF1_Any_Mutants", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                      "-oT=SKCM-NF1_Any_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=25, in cluster file=31, common to both=25
[1] "Reduce the number of clustering variables from 80 to 38."
[1] 38 25
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                21 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                21 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                16 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                21 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                21 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                22 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                22 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11                14 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11                14 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                15 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                16 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                20 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                19 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                19 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 21 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 21 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 21 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 21 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 20 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 22 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 22 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 6                 19 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 6                 19 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 17 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 16 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                22 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                22 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                21 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                21 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                21 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                21 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                21 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                21 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                19 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                19 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                15 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                15 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               16                 9 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               16                 9 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13                12 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13                12 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 17 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 17 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                 16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                 16 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 16 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 22 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 22 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 19 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                 22 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                 22 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 20 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 20 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 21 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 21 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 22 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 22 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                 18 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                 18 
[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 25 columns.

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

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    1  3
  1P GAIN WILD-TYPE  8 13
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                21 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                13 
$`1P GAIN MUTATED`
TCGA-EE-A29L TCGA-ER-A19F TCGA-FW-A3I3 TCGA-GN-A266 
        2.56        26.37         0.20        10.09 

$`1P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       18.58        25.87        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-FS-A1Z3 
      204.62        96.23       136.44        41.59        26.73        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       27.68        74.73        27.02 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.2              14.3 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            26.37            204.62 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            6.325            29.820 
[1] "0.2 - 26.4 (6.3)"    "14.3 - 204.6 (29.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-GN-A266 
  "1P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-GN-A266 
  "1P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-GN-A266 
  "1P GAIN MUTATED" 
[1] "hr=" "8.5"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS
  1P GAIN MUTATED                    1
  1P GAIN WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          1
  1P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                     2
  1P GAIN WILD-TYPE                  11
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    3
  1P GAIN WILD-TYPE    7   14
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               1                 7
  MALE                 3                14
                   vv
clus                N0 N1B N2C N3
  1P GAIN MUTATED    2   0   0  1
  1P GAIN WILD-TYPE 14   3   2  1
D1V5, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0                2                14
  N1B               0                 3
  N2C               0                 2
  N3                1                 1
D1V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  1P GAIN MUTATED          0        0        0         0          0          1
  1P GAIN WILD-TYPE        3        1        6         3          3          3
                   vv
clus                STAGE IV
  1P GAIN MUTATED          1
  1P GAIN WILD-TYPE        0
D1V7, multiclass
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                19 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29V        TCGA-EE-A2A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2GC        TCGA-EE-A2GO        TCGA-EE-A2GR        TCGA-EE-A2MI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A2MJ        TCGA-EE-A2MS        TCGA-EE-A2MT        TCGA-EE-A3AE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2               0 1
  1Q GAIN MUTATED   1 8
  1Q GAIN WILD-TYPE 8 8
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                 8 
$`1Q GAIN MUTATED`
TCGA-DA-A1IC TCGA-EE-A29L TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP 
       68.09         2.56        26.37        20.91        27.68        74.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.02         0.20        10.09 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       48.76        20.38        29.82        33.73        14.70        18.58 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI 
       25.87        24.43        43.23       101.95        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE 
       96.23       136.44        41.59        26.73 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.2              14.3 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            74.73            204.62 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           26.370            31.775 
[1] "0.2 - 74.7 (26.4)"   "14.3 - 204.6 (31.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A266 
  "1Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A266 
  "1Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A266 
  "1Q GAIN MUTATED" 
[1] "hr=" "3.4"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS
  1Q GAIN MUTATED                    4
  1Q GAIN WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                          2
  1Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                     3
  1Q GAIN WILD-TYPE                  10
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     10
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4    5
  1Q GAIN WILD-TYPE    4   12
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               4                 4
  MALE                 5                12
                   vv
clus                N0 N1B N2C N3
  1Q GAIN MUTATED    4   0   2  1
  1Q GAIN WILD-TYPE 12   3   0  1
D2V5, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                4                12
  N1B               0                 3
  N2C               2                 0
  N3                1                 1
D2V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED          0        0        1         1          2          1
  1Q GAIN WILD-TYPE        3        1        5         2          1          3
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          1
  1Q GAIN WILD-TYPE        0
D2V7, multiclass

Clustering(3) Variable = 3p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  2
  3P GAIN WILD-TYPE  7 14
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                21 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                14 
$`3P GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A29L TCGA-EE-A3AE TCGA-GN-A266 
       48.76         2.56        26.73        10.09 

$`3P GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N 
       20.38        68.09        29.82        33.73        14.70        18.58 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI 
       25.87        24.43        43.23       101.95        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       96.23       136.44        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       74.73        27.02         0.20 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.56              0.20 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            48.76            204.62 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            18.41             27.68 
[1] "2.6 - 48.8 (18.4)"  "0.2 - 204.6 (27.7)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3P GAIN MUTATED" 
[1] "hr=" "1.6"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS
  3P GAIN MUTATED                    1
  3P GAIN WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          1
  3P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     2
  3P GAIN WILD-TYPE                  11
D3V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    3
  3P GAIN WILD-TYPE    7   14
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                 7
  MALE                 3                14
                   vv
clus                N0 N1B N2C N3
  3P GAIN MUTATED    2   0   0  1
  3P GAIN WILD-TYPE 14   3   2  1
D3V5, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0                2                14
  N1B               0                 3
  N2C               0                 2
  N3                1                 1
D3V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  3P GAIN MUTATED          2        0        0         0          0          1
  3P GAIN WILD-TYPE        1        1        6         3          3          3
                   vv
clus                STAGE IV
  3P GAIN MUTATED          0
  3P GAIN WILD-TYPE        1
D3V7, multiclass

Clustering(4) Variable = 3q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2  3
  3Q GAIN WILD-TYPE  7 13
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                13 
$`3Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A3AE TCGA-GN-A266 
       48.76        14.70         2.56        26.73        10.09 

$`3Q GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A29V 
       20.38        68.09        29.82        33.73        18.58        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       24.43        43.23       101.95        14.30       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP 
      136.44        41.59        26.37        20.91        27.68        74.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.02         0.20 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             2.56              0.20 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            48.76            204.62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            14.70             28.75 
[1] "2.6 - 48.8 (14.7)"  "0.2 - 204.6 (28.8)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
  "3Q GAIN MUTATED" 
[1] "hr=" "2.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS
  3Q GAIN MUTATED                    2
  3Q GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          1
  3Q GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     2
  3Q GAIN WILD-TYPE                  11
D4V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    3
  3Q GAIN WILD-TYPE    6   14
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                 6
  MALE                 3                14
                   vv
clus                N0 N1B N2C N3
  3Q GAIN MUTATED    2   1   0  1
  3Q GAIN WILD-TYPE 14   2   2  1
D4V5, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                2                14
  N1B               1                 2
  N2C               0                 2
  N3                1                 1
D4V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED          2        0        0         0          0          2
  3Q GAIN WILD-TYPE        1        1        6         3          3          2
                   vv
clus                STAGE IV
  3Q GAIN MUTATED          0
  3Q GAIN WILD-TYPE        1
D4V7, multiclass

Clustering(5) Variable = 5p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    4  0
  5P GAIN WILD-TYPE  5 16
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                21 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                16 
$`5P GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FW-A3I3 
       48.76       136.44        26.73         0.20 

$`5P GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       20.38        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       18.58        25.87        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      204.62        96.23        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       74.73        27.02        10.09 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.20              2.56 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           136.44            204.62 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           37.745            27.020 
[1] "0.2 - 136.4 (37.7)" "2.6 - 204.6 (27.0)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-GN-A266 
"5P GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-GN-A266 
"5P GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-GN-A266 
"5P GAIN WILD-TYPE" 
[1] "hr="     "2.4e+08"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS
  5P GAIN MUTATED                    2
  5P GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P GAIN MUTATED                                                                                          0
  5P GAIN WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                     2
  5P GAIN WILD-TYPE                  11
D5V3, multiclass
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     11
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    2
  5P GAIN WILD-TYPE    6   15
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                 6
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  5P GAIN MUTATED    4   0   0  0
  5P GAIN WILD-TYPE 12   3   2  2
D5V5, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                4                12
  N1B               0                 3
  N2C               0                 2
  N3                0                 2
D5V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  5P GAIN MUTATED          2        0        1         0          0          0
  5P GAIN WILD-TYPE        1        1        5         3          3          4
                   vv
clus                STAGE IV
  5P GAIN MUTATED          1
  5P GAIN WILD-TYPE        0
D5V7, multiclass

Clustering(6) Variable = 5q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    3  0
  5Q GAIN WILD-TYPE  6 16
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                22 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                16 
$`5Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A2MS TCGA-EE-A3AE 
       48.76       136.44        26.73 

$`5Q GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       20.38        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       18.58        25.87        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      204.62        96.23        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            26.73              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           136.44            204.62 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           48.760            26.695 
[1] "26.7 - 136.4 (48.8)" "0.2 - 204.6 (26.7)" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
"5Q GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
"5Q GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A266 
"5Q GAIN WILD-TYPE" 
[1] "hr="     "2.4e+08"
D6V2, continuous
                   vv
clus                DISTANT METASTASIS
  5Q GAIN MUTATED                    1
  5Q GAIN WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q GAIN MUTATED                                                                                          0
  5Q GAIN WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  5Q GAIN MUTATED                     2
  5Q GAIN WILD-TYPE                  11
D6V3, multiclass
                                                                                          clus
vv                                                                                         5Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         5Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     11
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      1    2
  5Q GAIN WILD-TYPE    7   15
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               1                 7
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  5Q GAIN MUTATED    3   0   0  0
  5Q GAIN WILD-TYPE 13   3   2  2
D6V5, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                3                13
  N1B               0                 3
  N2C               0                 2
  N3                0                 2
D6V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  5Q GAIN MUTATED          2        0        1         0          0          0
  5Q GAIN WILD-TYPE        1        1        5         3          3          4
                   vv
clus                STAGE IV
  5Q GAIN MUTATED          0
  5Q GAIN WILD-TYPE        1
D6V7, multiclass

Clustering(7) Variable = 6p gain mutation analysis
D7V1, survival
                   sevent
clus2               0 1
  6P GAIN MUTATED   4 7
  6P GAIN WILD-TYPE 5 9
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11                14 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                 9 
$`6P GAIN MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MS 
       48.76        20.38        33.73        14.30       204.62       136.44 
TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       20.91        74.73        27.02         0.20        10.09 

$`6P GAIN WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V 
       68.09        29.82        14.70         2.56        18.58        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE 
       24.43        43.23       101.95        96.23        41.59        26.73 
TCGA-ER-A19F TCGA-FS-A1ZA 
       26.37        27.68 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.20              2.56 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           204.62            101.95 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           27.020            27.205 
[1] "0.2 - 204.6 (27.0)" "2.6 - 102.0 (27.2)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A266 
  "6P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A266 
  "6P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A266 
  "6P GAIN MUTATED" 
[1] "hr=" "1.2"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS
  6P GAIN MUTATED                    4
  6P GAIN WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          3
  6P GAIN WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                     4
  6P GAIN WILD-TYPE                   9
D7V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                      9
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    7
  6P GAIN WILD-TYPE    4   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               4                 4
  MALE                 7                10
                   vv
clus                N0 N1B N2C N3
  6P GAIN MUTATED    8   0   0  1
  6P GAIN WILD-TYPE  8   3   2  1
D7V5, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                8                 8
  N1B               0                 3
  N2C               0                 2
  N3                1                 1
D7V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  6P GAIN MUTATED          1        0        4         2          0          1
  6P GAIN WILD-TYPE        2        1        2         1          3          3
                   vv
clus                STAGE IV
  6P GAIN MUTATED          1
  6P GAIN WILD-TYPE        0
D7V7, multiclass

Clustering(8) Variable = 7p gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    4  6
  7P GAIN WILD-TYPE  5 10
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               10                15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                10 
$`7P GAIN MUTATED`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2GO TCGA-EE-A2MS 
       20.38        68.09        33.73        18.58       101.95       136.44 
TCGA-EE-A3AE TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       26.73        27.02         0.20        10.09 

$`7P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 
       48.76        29.82        14.70         2.56        25.87        24.43 
TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F 
       43.23        14.30       204.62        96.23        41.59        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP 
       20.91        27.68        74.73 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              2.56 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           136.44            204.62 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           26.875            27.680 
[1] "0.2 - 136.4 (26.9)" "2.6 - 204.6 (27.7)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A266 
  "7P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A266 
  "7P GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A266 
  "7P GAIN MUTATED" 
[1] "hr=" "1"  
D8V2, continuous
                   vv
clus                DISTANT METASTASIS
  7P GAIN MUTATED                    2
  7P GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                          4
  7P GAIN WILD-TYPE                                                                                        1
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                     4
  7P GAIN WILD-TYPE                   9
D8V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 1
  REGIONAL LYMPH NODE                                                                                      9
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    5
  7P GAIN WILD-TYPE    3   12
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               5                 3
  MALE                 5                12
                   vv
clus                N0 N1B N2C N3
  7P GAIN MUTATED    7   0   1  1
  7P GAIN WILD-TYPE  9   3   1  1
D8V5, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                7                 9
  N1B               0                 3
  N2C               1                 1
  N3                1                 1
D8V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  7P GAIN MUTATED          1        0        3         1          1          1
  7P GAIN WILD-TYPE        2        1        3         2          2          3
                   vv
clus                STAGE IV
  7P GAIN MUTATED          1
  7P GAIN WILD-TYPE        0
D8V7, multiclass

Clustering(9) Variable = 7q gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    4  5
  7Q GAIN WILD-TYPE  5 11
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                9                16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                11 
$`7Q GAIN MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2GO TCGA-EE-A2MS TCGA-EE-A3AE 
       68.09        33.73        18.58       101.95       136.44        26.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.02         0.20        10.09 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       48.76        20.38        29.82        14.70         2.56        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       24.43        43.23        14.30       204.62        96.23        41.59 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP 
       26.37        20.91        27.68        74.73 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              2.56 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           136.44            204.62 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           27.020            27.025 
[1] "0.2 - 136.4 (27.0)" "2.6 - 204.6 (27.0)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A266 
  "7Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A266 
  "7Q GAIN MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-GN-A266 
  "7Q GAIN MUTATED" 
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS
  7Q GAIN MUTATED                    2
  7Q GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                          3
  7Q GAIN WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                     4
  7Q GAIN WILD-TYPE                   9
D9V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                      9
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5    4
  7Q GAIN WILD-TYPE    3   13
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               5                 3
  MALE                 4                13
                   vv
clus                N0 N1B N2C N3
  7Q GAIN MUTATED    7   0   1  0
  7Q GAIN WILD-TYPE  9   3   1  2
D9V5, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                7                 9
  N1B               0                 3
  N2C               1                 1
  N3                0                 2
D9V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED          1        0        3         1          1          0
  7Q GAIN WILD-TYPE        2        1        3         2          2          4
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          1
  7Q GAIN WILD-TYPE        0
D9V7, multiclass

Clustering(10) Variable = 8p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    3  2
  8P GAIN WILD-TYPE  6 14
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                20 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                14 
$`8P GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A181 TCGA-EE-A2GO TCGA-FS-A1ZP TCGA-FW-A3I3 
       48.76        33.73       101.95        74.73         0.20 

$`8P GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       20.38        68.09        29.82        14.70         2.56        18.58 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       25.87        24.43        43.23        14.30       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      136.44        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZZ TCGA-GN-A266 
       27.02        10.09 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.20              2.56 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           101.95            204.62 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            48.76             26.55 
[1] "0.2 - 102.0 (48.8)" "2.6 - 204.6 (26.6)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A266 
"8P GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A266 
"8P GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A266 
"8P GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D10V2, continuous
                   vv
clus                DISTANT METASTASIS
  8P GAIN MUTATED                    2
  8P GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                          1
  8P GAIN WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                     2
  8P GAIN WILD-TYPE                  11
D10V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     11
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3    2
  8P GAIN WILD-TYPE    5   15
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               3                 5
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  8P GAIN MUTATED    5   0   0  0
  8P GAIN WILD-TYPE 11   3   2  2
D10V5, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                5                11
  N1B               0                 3
  N2C               0                 2
  N3                0                 2
D10V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  8P GAIN MUTATED          1        0        3         0          0          0
  8P GAIN WILD-TYPE        2        1        3         3          3          4
                   vv
clus                STAGE IV
  8P GAIN MUTATED          1
  8P GAIN WILD-TYPE        0
D10V7, multiclass

Clustering(11) Variable = 8q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    3  3
  8Q GAIN WILD-TYPE  6 13
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                6                19 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                13 
$`8Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A2GO TCGA-FS-A1ZP TCGA-FW-A3I3 
       48.76        20.38        33.73       101.95        74.73         0.20 

$`8Q GAIN WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V 
       68.09        29.82        14.70         2.56        18.58        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS 
       24.43        43.23        14.30       204.62        96.23       136.44 
TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZZ 
       41.59        26.73        26.37        20.91        27.68        27.02 
TCGA-GN-A266 
       10.09 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.20              2.56 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           101.95            204.62 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           41.245            26.730 
[1] "0.2 - 102.0 (41.2)" "2.6 - 204.6 (26.7)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A266 
"8Q GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A266 
"8Q GAIN WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A266 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS
  8Q GAIN MUTATED                    2
  8Q GAIN WILD-TYPE                  5
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                          2
  8Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                     2
  8Q GAIN WILD-TYPE                  11
D11V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     11
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    3
  8Q GAIN WILD-TYPE    5   14
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               3                 5
  MALE                 3                14
                   vv
clus                N0 N1B N2C N3
  8Q GAIN MUTATED    5   0   0  1
  8Q GAIN WILD-TYPE 11   3   2  1
D11V5, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                5                11
  N1B               0                 3
  N2C               0                 2
  N3                1                 1
D11V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED          1        0        3         0          0          1
  8Q GAIN WILD-TYPE        2        1        3         3          3          3
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          1
  8Q GAIN WILD-TYPE        0
D11V7, multiclass

Clustering(12) Variable = 14q gain mutation analysis
D12V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  2
  14Q GAIN WILD-TYPE  7 14
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 21 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                 14 
$`14Q GAIN MUTATED`
TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A3AE TCGA-FS-A1ZP 
        2.56       101.95        26.73        74.73 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        24.43        43.23        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       96.23       136.44        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.02         0.20        10.09 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.56               0.20 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            101.95             204.62 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             50.73              27.02 
[1] "2.6 - 102.0 (50.7)" "0.2 - 204.6 (27.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"14Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D12V2, continuous
                    vv
clus                 DISTANT METASTASIS
  14Q GAIN MUTATED                    0
  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                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                     3
  14Q GAIN WILD-TYPE                  10
D12V3, multiclass
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      10
D12V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2    2
  14Q GAIN WILD-TYPE    6   15
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                2                  6
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  14Q GAIN MUTATED    3   0   0  1
  14Q GAIN WILD-TYPE 13   3   2  1
D12V5, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                 3                 13
  N1B                0                  3
  N2C                0                  2
  N3                 1                  1
D12V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  14Q GAIN MUTATED          1        0        2         0          0          1
  14Q GAIN WILD-TYPE        2        1        4         3          3          3
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          0
  14Q GAIN WILD-TYPE        1
D12V7, multiclass

Clustering(13) Variable = 15q gain mutation analysis
D13V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    3  1
  15Q GAIN WILD-TYPE  6 15
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 21 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 15 
$`15Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GO TCGA-EE-A3AE TCGA-FS-A1Z3 
       48.76       101.95        26.73        20.91 

$`15Q GAIN WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       20.38        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        24.43        43.23        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZA TCGA-FS-A1ZP 
       96.23       136.44        41.59        26.37        27.68        74.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.02         0.20        10.09 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             20.91               0.20 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            101.95             204.62 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            37.745             27.020 
[1] "20.9 - 102.0 (37.7)" "0.2 - 204.6 (27.0)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"15Q GAIN WILD-TYPE" 
[1] "hr=" "3.3"
D13V2, continuous
                    vv
clus                 DISTANT METASTASIS
  15Q GAIN MUTATED                    2
  15Q GAIN WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          1
  15Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                     1
  15Q GAIN WILD-TYPE                  12
D13V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      12
D13V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    1
  15Q GAIN WILD-TYPE    5   16
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                  5
  MALE                  1                 16
                    vv
clus                 N0 N1B N2C N3
  15Q GAIN MUTATED    3   0   0  0
  15Q GAIN WILD-TYPE 13   3   2  2
D13V5, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                 3                 13
  N1B                0                  3
  N2C                0                  2
  N3                 0                  2
D13V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  15Q GAIN MUTATED          2        0        1         0          0          0
  15Q GAIN WILD-TYPE        1        1        5         3          3          4
                    vv
clus                 STAGE IV
  15Q GAIN MUTATED          0
  15Q GAIN WILD-TYPE        1
D13V7, multiclass

Clustering(14) Variable = 17q gain mutation analysis
D14V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    1  4
  17Q GAIN WILD-TYPE  8 12
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 12 
$`17Q GAIN MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A3AE 
       68.09        33.73         2.56        18.58        26.73 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2A2 
       48.76        20.38        29.82        14.70        25.87        24.43 
TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS 
       43.23       101.95        14.30       204.62        96.23       136.44 
TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       41.59        26.37        20.91        27.68        74.73        27.02 
TCGA-FW-A3I3 TCGA-GN-A266 
        0.20        10.09 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              2.56               0.20 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             68.09             204.62 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             26.73              27.35 
[1] "2.6 - 68.1 (26.7)"  "0.2 - 204.6 (27.4)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266 
"17Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D14V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17Q GAIN MUTATED                    0
  17Q GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          1
  17Q GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                     4
  17Q GAIN WILD-TYPE                   9
D14V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                       9
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    3
  17Q GAIN WILD-TYPE    6   14
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                  6
  MALE                  3                 14
                    vv
clus                 N0 N1B N2C N3
  17Q GAIN MUTATED    3   0   1  1
  17Q GAIN WILD-TYPE 13   3   1  1
D14V5, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                 3                 13
  N1B                0                  3
  N2C                1                  1
  N3                 1                  1
D14V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED          1        0        1         0          1          1
  17Q GAIN WILD-TYPE        2        1        5         3          2          3
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          0
  17Q GAIN WILD-TYPE        1
D14V7, multiclass

Clustering(15) Variable = 18p gain mutation analysis
D15V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    0  3
  18P GAIN WILD-TYPE  9 13
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 22 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 13 
$`18P GAIN MUTATED`
TCGA-DA-A1I0 TCGA-EE-A181 TCGA-EE-A29L 
       20.38        33.73         2.56 

$`18P GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
       48.76        68.09        29.82        14.70        18.58        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       24.43        43.23       101.95        14.30       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      136.44        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              2.56               0.20 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             33.73             204.62 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             20.38              27.35 
[1] "2.6 - 33.7 (20.4)"  "0.2 - 204.6 (27.4)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266 
"18P GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266 
"18P GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266 
"18P GAIN WILD-TYPE" 
[1] "hr=" "3.5"
D15V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18P GAIN MUTATED                    0
  18P GAIN WILD-TYPE                  7
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          1
  18P GAIN WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                     2
  18P GAIN WILD-TYPE                  11
D15V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      11
D15V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    2
  18P GAIN WILD-TYPE    7   15
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                  7
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  18P GAIN MUTATED    1   0   0  2
  18P GAIN WILD-TYPE 15   3   2  0
D15V5, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                 1                 15
  N1B                0                  3
  N2C                0                  2
  N3                 2                  0
D15V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  18P GAIN MUTATED          0        0        1         0          0          2
  18P GAIN WILD-TYPE        3        1        5         3          3          2
                    vv
clus                 STAGE IV
  18P GAIN MUTATED          0
  18P GAIN WILD-TYPE        1
D15V7, multiclass

Clustering(16) Variable = 20p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    4  2
  20P GAIN WILD-TYPE  5 14
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 6                 19 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 14 
$`20P GAIN MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A2GO TCGA-EE-A3AE TCGA-FS-A1ZA TCGA-FW-A3I3 
       48.76        20.38       101.95        26.73        27.68         0.20 

$`20P GAIN WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       68.09        29.82        33.73        14.70         2.56        18.58 
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       25.87        24.43        43.23        14.30       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ 
      136.44        41.59        26.37        20.91        74.73        27.02 
TCGA-GN-A266 
       10.09 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.20               2.56 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            101.95             204.62 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            27.205             27.020 
[1] "0.2 - 102.0 (27.2)" "2.6 - 204.6 (27.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A266 
"20P GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A266 
"20P GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A266 
"20P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D16V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20P GAIN MUTATED                    3
  20P GAIN WILD-TYPE                  4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                          2
  20P GAIN WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                     1
  20P GAIN WILD-TYPE                  12
D16V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      12
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4    2
  20P GAIN WILD-TYPE    4   15
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                4                  4
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  20P GAIN MUTATED    4   0   1  1
  20P GAIN WILD-TYPE 12   3   1  1
D16V5, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                 4                 12
  N1B                0                  3
  N2C                1                  1
  N3                 1                  1
D16V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  20P GAIN MUTATED          2        0        1         0          1          1
  20P GAIN WILD-TYPE        1        1        5         3          2          3
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          1
  20P GAIN WILD-TYPE        0
D16V7, multiclass

Clustering(17) Variable = 20q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    5  3
  20Q GAIN WILD-TYPE  4 13
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 13 
$`20Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A29L TCGA-EE-A2GO TCGA-EE-A2MS TCGA-EE-A3AE 
       48.76        20.38         2.56       101.95       136.44        26.73 
TCGA-FS-A1ZA TCGA-FW-A3I3 
       27.68         0.20 

$`20Q GAIN WILD-TYPE`
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29N TCGA-EE-A29V 
       68.09        29.82        33.73        14.70        18.58        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       24.43        43.23        14.30       204.62        96.23        41.59 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       26.37        20.91        74.73        27.02        10.09 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20              10.09 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            136.44             204.62 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            27.205             27.020 
[1] "0.2 - 136.4 (27.2)"  "10.1 - 204.6 (27.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A266 
"20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A266 
"20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A266 
"20Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D17V2, continuous
                    vv
clus                 DISTANT METASTASIS
  20Q GAIN MUTATED                    3
  20Q GAIN WILD-TYPE                  4
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                          2
  20Q GAIN WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                     3
  20Q GAIN WILD-TYPE                  10
D17V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      10
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    4
  20Q GAIN WILD-TYPE    4   13
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                  4
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  20Q GAIN MUTATED    5   0   1  2
  20Q GAIN WILD-TYPE 11   3   1  0
D17V5, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                 5                 11
  N1B                0                  3
  N2C                1                  1
  N3                 2                  0
D17V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED          2        0        2         0          1          2
  20Q GAIN WILD-TYPE        1        1        4         3          2          2
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          1
  20Q GAIN WILD-TYPE        0
D17V7, multiclass

Clustering(18) Variable = 22q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  5
  22Q GAIN WILD-TYPE  5 11
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 16 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 11 
$`22Q GAIN MUTATED`
TCGA-DA-A1I0 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2GO TCGA-EE-A2MJ TCGA-EE-A2MS 
       20.38         2.56        18.58       101.95        96.23       136.44 
TCGA-EE-A3AE TCGA-FS-A1ZA TCGA-FW-A3I3 
       26.73        27.68         0.20 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29V 
       48.76        68.09        29.82        33.73        14.70        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MT TCGA-ER-A19F 
       24.43        43.23        14.30       204.62        41.59        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       20.91        74.73        27.02        10.09 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20              10.09 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            136.44             204.62 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             26.73              28.42 
[1] "0.2 - 136.4 (26.7)"  "10.1 - 204.6 (28.4)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A266 
"22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A266 
"22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A266 
"22Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D18V2, continuous
                    vv
clus                 DISTANT METASTASIS
  22Q GAIN MUTATED                    2
  22Q GAIN WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                          2
  22Q GAIN WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                     5
  22Q GAIN WILD-TYPE                   8
D18V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                       8
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    5
  22Q GAIN WILD-TYPE    4   12
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                  4
  MALE                  5                 12
                    vv
clus                 N0 N1B N2C N3
  22Q GAIN MUTATED    6   0   1  2
  22Q GAIN WILD-TYPE 10   3   1  0
D18V5, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                 6                 10
  N1B                0                  3
  N2C                1                  1
  N3                 2                  0
D18V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED          1        0        3         0          1          2
  22Q GAIN WILD-TYPE        2        1        3         3          2          2
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          1
  22Q GAIN WILD-TYPE        0
D18V7, multiclass

Clustering(19) Variable = 1p loss mutation analysis
D19V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    3  0
  1P LOSS WILD-TYPE  6 16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                22 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                16 
$`1P LOSS MUTATED`
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MS 
      101.95        14.30       136.44 

$`1P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MI 
        2.56        18.58        25.87        24.43        43.23       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       96.23        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             14.3               0.2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           136.44            204.62 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
          101.950            26.875 
[1] "14.3 - 136.4 (102.0)" "0.2 - 204.6 (26.9)"  
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A266 
"1P LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A266 
"1P LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A266 
"1P LOSS WILD-TYPE" 
[1] "hr="   "3e+08"
D19V2, continuous
                   vv
clus                DISTANT METASTASIS
  1P LOSS MUTATED                    0
  1P LOSS WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          2
  1P LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     1
  1P LOSS WILD-TYPE                  12
D19V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     12
D19V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE    7   15
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                 7
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  1P LOSS MUTATED    3   0   0  0
  1P LOSS WILD-TYPE 13   3   2  2
D19V5, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0                3                13
  N1B               0                 3
  N2C               0                 2
  N3                0                 2
D19V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  1P LOSS MUTATED          0        0        3         0          0          0
  1P LOSS WILD-TYPE        3        1        3         3          3          4
                   vv
clus                STAGE IV
  1P LOSS MUTATED          0
  1P LOSS WILD-TYPE        1
D19V7, multiclass

Clustering(20) Variable = 4p loss mutation analysis
D20V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    2  2
  4P LOSS WILD-TYPE  7 14
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                21 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                14 
$`4P LOSS MUTATED`
TCGA-EE-A2GO TCGA-EE-A2MS TCGA-FS-A1ZA TCGA-GN-A266 
      101.95       136.44        27.68        10.09 

$`4P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR 
        2.56        18.58        25.87        24.43        43.23        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
      204.62        96.23        41.59        26.73        26.37        20.91 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       74.73        27.02         0.20 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            10.09              0.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           136.44            204.62 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           64.815            26.730 
[1] "10.1 - 136.4 (64.8)" "0.2 - 204.6 (26.7)" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4P LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4P LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4P LOSS MUTATED" 
[1] "hr=" "2"  
D20V2, continuous
                   vv
clus                DISTANT METASTASIS
  4P LOSS MUTATED                    1
  4P LOSS WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          2
  4P LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     1
  4P LOSS WILD-TYPE                  12
D20V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     12
D20V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    2
  4P LOSS WILD-TYPE    6   15
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               2                 6
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  4P LOSS MUTATED    2   0   1  0
  4P LOSS WILD-TYPE 14   3   1  2
D20V5, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                2                14
  N1B               0                 3
  N2C               1                 1
  N3                0                 2
D20V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  4P LOSS MUTATED          0        0        2         0          1          0
  4P LOSS WILD-TYPE        3        1        4         3          2          4
                   vv
clus                STAGE IV
  4P LOSS MUTATED          0
  4P LOSS WILD-TYPE        1
D20V7, multiclass

Clustering(21) Variable = 4q loss mutation analysis
D21V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    2  2
  4Q LOSS WILD-TYPE  7 14
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                21 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                14 
$`4Q LOSS MUTATED`
TCGA-EE-A181 TCGA-EE-A2GO TCGA-EE-A2MS TCGA-GN-A266 
       33.73       101.95       136.44        10.09 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L 
       48.76        20.38        68.09        29.82        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        24.43        43.23        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       96.23        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       74.73        27.02         0.20 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            10.09              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           136.44            204.62 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            67.84             26.73 
[1] "10.1 - 136.4 (67.8)" "0.2 - 204.6 (26.7)" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4Q LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4Q LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "4Q LOSS MUTATED" 
[1] "hr=" "2.2"
D21V2, continuous
                   vv
clus                DISTANT METASTASIS
  4Q LOSS MUTATED                    0
  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                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                     2
  4Q LOSS WILD-TYPE                  11
D21V3, multiclass
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     11
D21V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    2
  4Q LOSS WILD-TYPE    6   15
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               2                 6
  MALE                 2                15
                   vv
clus                N0 N1B N2C N3
  4Q LOSS MUTATED    3   0   0  0
  4Q LOSS WILD-TYPE 13   3   2  2
D21V5, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0                3                13
  N1B               0                 3
  N2C               0                 2
  N3                0                 2
D21V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED          0        0        3         0          0          0
  4Q LOSS WILD-TYPE        3        1        3         3          3          4
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        1
D21V7, multiclass

Clustering(22) Variable = 5p loss mutation analysis
D22V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    2  2
  5P LOSS WILD-TYPE  7 14
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                21 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                14 
$`5P LOSS MUTATED`
TCGA-EE-A17X TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-GN-A266 
       29.82        24.43        14.30        10.09 

$`5P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       48.76        20.38        68.09        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MJ 
       18.58        25.87        43.23       101.95       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      136.44        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       74.73        27.02         0.20 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            10.09              0.20 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            29.82            204.62 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           19.365            27.680 
[1] "10.1 - 29.8 (19.4)" "0.2 - 204.6 (27.7)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5P LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5P LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5P LOSS MUTATED" 
[1] "hr=" "2"  
D22V2, continuous
                   vv
clus                DISTANT METASTASIS
  5P LOSS MUTATED                    0
  5P LOSS WILD-TYPE                  7
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          2
  5P LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                     2
  5P LOSS WILD-TYPE                  11
D22V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     11
D22V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    4
  5P LOSS WILD-TYPE    8   13
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               0                 8
  MALE                 4                13
                   vv
clus                N0 N1B N2C N3
  5P LOSS MUTATED    2   1   0  0
  5P LOSS WILD-TYPE 14   2   2  2
D22V5, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                2                14
  N1B               1                 2
  N2C               0                 2
  N3                0                 2
D22V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  5P LOSS MUTATED          1        0        1         0          1          0
  5P LOSS WILD-TYPE        2        1        5         3          2          4
                   vv
clus                STAGE IV
  5P LOSS MUTATED          0
  5P LOSS WILD-TYPE        1
D22V7, multiclass

Clustering(23) Variable = 5q loss mutation analysis
D23V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    2  4
  5Q LOSS WILD-TYPE  7 12
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                19 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                12 
$`5Q LOSS MUTATED`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-GN-A266 
       20.38        29.82        25.87        24.43        14.30        10.09 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29N 
       48.76        68.09        33.73        14.70         2.56        18.58 
TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT 
       43.23       101.95       204.62        96.23       136.44        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       26.73        26.37        20.91        27.68        74.73        27.02 
TCGA-FW-A3I3 
        0.20 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            10.09              0.20 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            29.82            204.62 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           22.405            33.730 
[1] "10.1 - 29.8 (22.4)" "0.2 - 204.6 (33.7)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5Q LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5Q LOSS MUTATED" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A266 
  "5Q LOSS MUTATED" 
[1] "hr=" "3.3"
D23V2, continuous
                   vv
clus                DISTANT METASTASIS
  5Q LOSS MUTATED                    1
  5Q LOSS WILD-TYPE                  6
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          3
  5Q LOSS WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                     2
  5Q LOSS WILD-TYPE                  11
D23V3, multiclass
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                     11
D23V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    6
  5Q LOSS WILD-TYPE    8   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               0                 8
  MALE                 6                11
                   vv
clus                N0 N1B N2C N3
  5Q LOSS MUTATED    2   2   0  1
  5Q LOSS WILD-TYPE 14   1   2  1
D23V5, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                2                14
  N1B               2                 1
  N2C               0                 2
  N3                1                 1
D23V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED          1        0        1         0          1          2
  5Q LOSS WILD-TYPE        2        1        5         3          2          2
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          0
  5Q LOSS WILD-TYPE        1
D23V7, multiclass

Clustering(24) Variable = 6q loss mutation analysis
D24V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    5  5
  6Q LOSS WILD-TYPE  4 11
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                15 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                11 
$`6Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2A2 
       48.76        68.09        33.73        14.70        25.87        24.43 
TCGA-EE-A2GO TCGA-EE-A2MT TCGA-ER-A19F TCGA-FW-A3I3 
      101.95        41.59        26.37         0.20 

$`6Q LOSS WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GR 
       20.38        29.82         2.56        18.58        43.23        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      204.62        96.23       136.44        26.73        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       74.73        27.02        10.09 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.20              2.56 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           101.95            204.62 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            30.05             27.02 
[1] "0.2 - 102.0 (30.0)" "2.6 - 204.6 (27.0)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A266 
"6Q LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A266 
"6Q LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-GN-A266 
"6Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D24V2, continuous
                   vv
clus                DISTANT METASTASIS
  6Q LOSS MUTATED                    4
  6Q LOSS WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                          2
  6Q LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                     4
  6Q LOSS WILD-TYPE                   9
D24V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                      9
D24V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      4    6
  6Q LOSS WILD-TYPE    4   11
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               4                 4
  MALE                 6                11
                   vv
clus                N0 N1B N2C N3
  6Q LOSS MUTATED    6   3   1  0
  6Q LOSS WILD-TYPE 10   0   1  2
D24V5, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                6                10
  N1B               3                 0
  N2C               1                 1
  N3                0                 2
D24V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED          1        1        2         0          2          2
  6Q LOSS WILD-TYPE        2        0        4         3          1          2
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          1
  6Q LOSS WILD-TYPE        0
D24V7, multiclass

Clustering(25) Variable = 9p loss mutation analysis
D25V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    6 10
  9P LOSS WILD-TYPE  3  6
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               16                 9 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                 6 
$`9P LOSS MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       48.76        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MS 
       18.58        25.87        43.23       101.95        14.30       136.44 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FW-A3I3 
       26.37        20.91        27.68         0.20 

$`9P LOSS WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A2A2 TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE 
       20.38        24.43       204.62        96.23        41.59        26.73 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       74.73        27.02        10.09 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.20             10.09 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           136.44            204.62 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           27.025            27.020 
[1] "0.2 - 136.4 (27.0)"  "10.1 - 204.6 (27.0)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A266 
"9P LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A266 
"9P LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A266 
"9P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D25V2, continuous
                   vv
clus                DISTANT METASTASIS
  9P LOSS MUTATED                    6
  9P LOSS WILD-TYPE                  1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                          3
  9P LOSS WILD-TYPE                                                                                        2
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                     7
  9P LOSS WILD-TYPE                   6
D25V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                     6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
  REGIONAL LYMPH NODE                                                                                      6
D25V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   10
  9P LOSS WILD-TYPE    2    7
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               6                 2
  MALE                10                 7
                   vv
clus                N0 N1B N2C N3
  9P LOSS MUTATED   10   2   2  1
  9P LOSS WILD-TYPE  6   1   0  1
D25V5, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0               10                 6
  N1B               2                 1
  N2C               2                 0
  N3                1                 1
D25V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  9P LOSS MUTATED          2        0        4         1          2          3
  9P LOSS WILD-TYPE        1        1        2         2          1          1
                   vv
clus                STAGE IV
  9P LOSS MUTATED          1
  9P LOSS WILD-TYPE        0
D25V7, multiclass

Clustering(26) Variable = 9q loss mutation analysis
D26V1, survival
                   sevent
clus2               0 1
  9Q LOSS MUTATED   5 8
  9Q LOSS WILD-TYPE 4 8
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13                12 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                 8 
$`9Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 
       48.76        68.09        33.73         2.56        18.58        24.43 
TCGA-EE-A2GC TCGA-EE-A2MS TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA TCGA-FS-A1ZZ 
       43.23       136.44        26.37        20.91        27.68        27.02 
TCGA-FW-A3I3 
        0.20 

$`9Q LOSS WILD-TYPE`
TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29V TCGA-EE-A2GO TCGA-EE-A2GR 
       20.38        29.82        14.70        25.87       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE TCGA-FS-A1ZP TCGA-GN-A266 
      204.62        96.23        41.59        26.73        74.73        10.09 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.20             10.09 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           136.44            204.62 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           27.020            28.275 
[1] "0.2 - 136.4 (27.0)"  "10.1 - 204.6 (28.3)"
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A266 
"9Q LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A266 
"9Q LOSS WILD-TYPE" 
       TCGA-D3-A2JF        TCGA-DA-A1I0        TCGA-DA-A1IC        TCGA-EE-A17X 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A182        TCGA-EE-A29L        TCGA-EE-A29N 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29V        TCGA-EE-A2A2        TCGA-EE-A2GC        TCGA-EE-A2GO 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A2GR        TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MS 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-ER-A19F        TCGA-FS-A1Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A1ZA        TCGA-FS-A1ZP        TCGA-FS-A1ZZ        TCGA-FW-A3I3 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-GN-A266 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D26V2, continuous
                   vv
clus                DISTANT METASTASIS
  9Q LOSS MUTATED                    5
  9Q LOSS WILD-TYPE                  2
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                          1
  9Q LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                     7
  9Q LOSS WILD-TYPE                   6
D26V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                      6
D26V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    8
  9Q LOSS WILD-TYPE    3    9
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               5                 3
  MALE                 8                 9
                   vv
clus                N0 N1B N2C N3
  9Q LOSS MUTATED    8   1   2  1
  9Q LOSS WILD-TYPE  8   2   0  1
D26V5, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                8                 8
  N1B               1                 2
  N2C               2                 0
  N3                1                 1
D26V6, continuous
                   vv
clus                STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED          1        0        2         2          3          1
  9Q LOSS WILD-TYPE        2        1        4         1          0          3
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          1
  9Q LOSS WILD-TYPE        0
D26V7, multiclass

Clustering(27) Variable = 10p loss mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    4  4
  10P LOSS WILD-TYPE  5 12
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 12 
$`10P LOSS MUTATED`
TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1Z3 
        2.56        43.23       101.95       136.44        26.73        20.91 
TCGA-FS-A1ZA TCGA-GN-A266 
       27.68        10.09 

$`10P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       18.58        25.87        24.43        14.30       204.62        96.23 
TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       41.59        26.37        74.73        27.02         0.20 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              2.56               0.20 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            136.44             204.62 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            27.205             27.020 
[1] "2.6 - 136.4 (27.2)" "0.2 - 204.6 (27.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10P LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10P LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10P LOSS MUTATED" 
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10P LOSS MUTATED                    2
  10P LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                          2
  10P LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                     4
  10P LOSS WILD-TYPE                   9
D27V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                       9
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    4
  10P LOSS WILD-TYPE    4   13
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                4                  4
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  10P LOSS MUTATED    4   0   1  1
  10P LOSS WILD-TYPE 12   3   1  1
D27V5, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                 4                 12
  N1B                0                  3
  N2C                1                  1
  N3                 1                  1
D27V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  10P LOSS MUTATED          1        0        2         1          1          1
  10P LOSS WILD-TYPE        2        1        4         2          2          3
                    vv
clus                 STAGE IV
  10P LOSS MUTATED          0
  10P LOSS WILD-TYPE        1
D27V7, multiclass

Clustering(28) Variable = 10q loss mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    3  5
  10Q LOSS WILD-TYPE  6 11
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 8                 17 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 11 
$`10Q LOSS MUTATED`
TCGA-EE-A29L TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MI TCGA-EE-A3AE TCGA-FS-A1Z3 
        2.56        43.23       101.95       204.62        26.73        20.91 
TCGA-FS-A1ZA TCGA-GN-A266 
       27.68        10.09 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-EE-A2MJ TCGA-EE-A2MS 
       18.58        25.87        24.43        14.30        96.23       136.44 
TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       41.59        26.37        74.73        27.02         0.20 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.56               0.20 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            204.62             136.44 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            27.205             27.020 
[1] "2.6 - 204.6 (27.2)" "0.2 - 136.4 (27.0)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "10Q LOSS MUTATED" 
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS
  10Q LOSS MUTATED                    2
  10Q LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                          2
  10Q LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                     4
  10Q LOSS WILD-TYPE                   9
D28V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                       9
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    4
  10Q LOSS WILD-TYPE    4   13
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                4                  4
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  10Q LOSS MUTATED    4   0   1  1
  10Q LOSS WILD-TYPE 12   3   1  1
D28V5, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                 4                 12
  N1B                0                  3
  N2C                1                  1
  N3                 1                  1
D28V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED          1        0        1         2          1          1
  10Q LOSS WILD-TYPE        2        1        5         1          2          3
                    vv
clus                 STAGE IV
  10Q LOSS MUTATED          0
  10Q LOSS WILD-TYPE        1
D28V7, multiclass

Clustering(29) Variable = 11p loss mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    5  4
  11P LOSS WILD-TYPE  4 12
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                 16 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 4                 12 
$`11P LOSS MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MS 
       14.70         2.56        25.87        24.43        43.23       136.44 
TCGA-EE-A3AE TCGA-FS-A1ZA TCGA-FW-A3I3 
       26.73        27.68         0.20 

$`11P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       48.76        20.38        68.09        29.82        33.73        18.58 
TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F 
      101.95        14.30       204.62        96.23        41.59        26.37 
TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-GN-A266 
       20.91        74.73        27.02        10.09 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20              10.09 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            136.44             204.62 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            25.870             31.775 
[1] "0.2 - 136.4 (25.9)"  "10.1 - 204.6 (31.8)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A266 
"11P LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A266 
"11P LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A266 
"11P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11P LOSS MUTATED                    4
  11P LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                          0
  11P LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                     5
  11P LOSS WILD-TYPE                   8
D29V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4    5
  11P LOSS WILD-TYPE    4   12
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                4                  4
  MALE                  5                 12
                    vv
clus                 N0 N1B N2C N3
  11P LOSS MUTATED    4   3   1  1
  11P LOSS WILD-TYPE 12   0   1  1
D29V5, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                 4                 12
  N1B                3                  0
  N2C                1                  1
  N3                 1                  1
D29V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  11P LOSS MUTATED          1        0        1         1          2          3
  11P LOSS WILD-TYPE        2        1        5         2          1          1
                    vv
clus                 STAGE IV
  11P LOSS MUTATED          1
  11P LOSS WILD-TYPE        0
D29V7, multiclass

Clustering(30) Variable = 11q loss mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    5  4
  11Q LOSS WILD-TYPE  4 12
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 16 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 4                 12 
$`11Q LOSS MUTATED`
TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2MT TCGA-EE-A3AE 
       14.70         2.56        24.43        43.23        41.59        26.73 
TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-FW-A3I3 
       27.68        27.02         0.20 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A29N 
       48.76        20.38        68.09        29.82        33.73        18.58 
TCGA-EE-A29V TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MS 
       25.87       101.95        14.30       204.62        96.23       136.44 
TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-GN-A266 
       26.37        20.91        74.73        10.09 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.20              10.09 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             43.23             204.62 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            26.730             31.775 
[1] "0.2 - 43.2 (26.7)"   "10.1 - 204.6 (31.8)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-GN-A266 
"11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-GN-A266 
"11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-GN-A266 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS
  11Q LOSS MUTATED                    4
  11Q LOSS WILD-TYPE                  3
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          0
  11Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                     5
  11Q LOSS WILD-TYPE                   8
D30V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                       8
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      5    4
  11Q LOSS WILD-TYPE    3   13
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                5                  3
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  11Q LOSS MUTATED    5   2   1  1
  11Q LOSS WILD-TYPE 11   1   1  1
D30V5, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                 5                 11
  N1B                2                  1
  N2C                1                  1
  N3                 1                  1
D30V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED          1        1        0         2          2          2
  11Q LOSS WILD-TYPE        2        0        6         1          1          2
                    vv
clus                 STAGE IV
  11Q LOSS MUTATED          1
  11Q LOSS WILD-TYPE        0
D30V7, multiclass

Clustering(31) Variable = 12q loss mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE  7 15
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 22 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 15 
$`12Q LOSS MUTATED`
TCGA-EE-A2A2 TCGA-EE-A2GR TCGA-FS-A1ZA 
       24.43        14.30        27.68 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MI 
        2.56        18.58        25.87        43.23       101.95       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
       96.23       136.44        41.59        26.73        26.37        20.91 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              14.3                0.2 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             27.68             204.62 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             24.43              28.42 
[1] "14.3 - 27.7 (24.4)" "0.2 - 204.6 (28.4)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS
  12Q LOSS MUTATED                    1
  12Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          1
  12Q LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     1
  12Q LOSS WILD-TYPE                  12
D31V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      12
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    2
  12Q LOSS WILD-TYPE    7   15
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                  7
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  12Q LOSS MUTATED    1   1   1  0
  12Q LOSS WILD-TYPE 15   2   1  2
D31V5, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                 1                 15
  N1B                1                  2
  N2C                1                  1
  N3                 0                  2
D31V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  12Q LOSS MUTATED          0        0        1         0          2          0
  12Q LOSS WILD-TYPE        3        1        5         3          1          4
                    vv
clus                 STAGE IV
  12Q LOSS MUTATED          0
  12Q LOSS WILD-TYPE        1
D31V7, multiclass

Clustering(32) Variable = 13q loss mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    1  5
  13Q LOSS WILD-TYPE  8 11
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 19 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 11 
$`13Q LOSS MUTATED`
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29N TCGA-EE-A2MS TCGA-FS-A1ZA TCGA-GN-A266 
       68.09        33.73        18.58       136.44        27.68        10.09 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L TCGA-EE-A29V 
       48.76        20.38        29.82        14.70         2.56        25.87 
TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
       24.43        43.23       101.95        14.30       204.62        96.23 
TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       41.59        26.73        26.37        20.91        74.73        27.02 
TCGA-FW-A3I3 
        0.20 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.09               0.20 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            136.44             204.62 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            30.705             26.730 
[1] "10.1 - 136.4 (30.7)" "0.2 - 204.6 (26.7)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "13Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "13Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "13Q LOSS MUTATED" 
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS
  13Q LOSS MUTATED                    1
  13Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          2
  13Q LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                     3
  13Q LOSS WILD-TYPE                  10
D32V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      10
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    4
  13Q LOSS WILD-TYPE    6   13
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                2                  6
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  13Q LOSS MUTATED    3   0   2  0
  13Q LOSS WILD-TYPE 13   3   0  2
D32V5, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                 3                 13
  N1B                0                  3
  N2C                2                  0
  N3                 0                  2
D32V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED          0        0        2         0          2          0
  13Q LOSS WILD-TYPE        3        1        4         3          1          4
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          0
  13Q LOSS WILD-TYPE        1
D32V7, multiclass

Clustering(33) Variable = 14q loss mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    1  2
  14Q LOSS WILD-TYPE  8 14
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                 22 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 14 
$`14Q LOSS MUTATED`
TCGA-EE-A181 TCGA-EE-A2MS TCGA-FS-A1ZA 
       33.73       136.44        27.68 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L 
       48.76        20.38        68.09        29.82        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2GR 
       18.58        25.87        24.43        43.23       101.95        14.30 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
      204.62        96.23        41.59        26.73        26.37        20.91 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             27.68               0.20 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            136.44             204.62 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             33.73              26.55 
[1] "27.7 - 136.4 (33.7)" "0.2 - 204.6 (26.6)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"14Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D33V2, continuous
                    vv
clus                 DISTANT METASTASIS
  14Q LOSS MUTATED                    1
  14Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                          0
  14Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                     2
  14Q LOSS WILD-TYPE                  11
D33V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      11
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2    1
  14Q LOSS WILD-TYPE    6   16
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                2                  6
  MALE                  1                 16
                    vv
clus                 N0 N1B N2C N3
  14Q LOSS MUTATED    2   0   1  0
  14Q LOSS WILD-TYPE 14   3   1  2
D33V5, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                 2                 14
  N1B                0                  3
  N2C                1                  1
  N3                 0                  2
D33V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED          0        0        2         0          1          0
  14Q LOSS WILD-TYPE        3        1        4         3          2          4
                    vv
clus                 STAGE IV
  14Q LOSS MUTATED          0
  14Q LOSS WILD-TYPE        1
D33V7, multiclass

Clustering(34) Variable = 16q loss mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    3  1
  16Q LOSS WILD-TYPE  6 15
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 21 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 15 
$`16Q LOSS MUTATED`
TCGA-D3-A2JF TCGA-EE-A2GC TCGA-FS-A1ZP TCGA-FW-A3I3 
       48.76        43.23        74.73         0.20 

$`16Q LOSS WILD-TYPE`
TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A29L 
       20.38        68.09        29.82        33.73        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI 
       18.58        25.87        24.43       101.95        14.30       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 
       96.23       136.44        41.59        26.73        26.37        20.91 
TCGA-FS-A1ZA TCGA-FS-A1ZZ TCGA-GN-A266 
       27.68        27.02        10.09 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.20               2.56 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             74.73             204.62 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            45.995             26.730 
[1] "0.2 - 74.7 (46.0)"  "2.6 - 204.6 (26.7)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A266 
"16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A266 
"16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A266 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "3.1"
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS
  16Q LOSS MUTATED                    2
  16Q LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          0
  16Q LOSS WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                     2
  16Q LOSS WILD-TYPE                  11
D34V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      11
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    3
  16Q LOSS WILD-TYPE    7   14
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                1                  7
  MALE                  3                 14
                    vv
clus                 N0 N1B N2C N3
  16Q LOSS MUTATED    4   0   0  0
  16Q LOSS WILD-TYPE 12   3   2  2
D34V5, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                 4                 12
  N1B                0                  3
  N2C                0                  2
  N3                 0                  2
D34V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED          1        0        1         1          0          0
  16Q LOSS WILD-TYPE        2        1        5         2          3          4
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          1
  16Q LOSS WILD-TYPE        0
D34V7, multiclass

Clustering(35) Variable = 17p loss mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    3  2
  17P LOSS WILD-TYPE  6 14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 20 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 14 
$`17P LOSS MUTATED`
TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-FW-A3I3 TCGA-GN-A266 
       25.87        24.43        43.23         0.20        10.09 

$`17P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2GO TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ 
        2.56        18.58       101.95        14.30       204.62        96.23 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
      136.44        41.59        26.73        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ 
       74.73        27.02 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               2.56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             43.23             204.62 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             24.43              28.75 
[1] "0.2 - 43.2 (24.4)"  "2.6 - 204.6 (28.8)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A266 
  "17P LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A266 
  "17P LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A266 
  "17P LOSS MUTATED" 
[1] "hr=" "1.4"
D35V2, continuous
                    vv
clus                 DISTANT METASTASIS
  17P LOSS MUTATED                    2
  17P LOSS WILD-TYPE                  5
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          1
  17P LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                     2
  17P LOSS WILD-TYPE                  11
D35V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      11
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    4
  17P LOSS WILD-TYPE    7   13
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                1                  7
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  17P LOSS MUTATED    2   2   0  0
  17P LOSS WILD-TYPE 14   1   2  2
D35V5, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0                 2                 14
  N1B                2                  1
  N2C                0                  2
  N3                 0                  2
D35V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  17P LOSS MUTATED          0        0        0         1          1          1
  17P LOSS WILD-TYPE        3        1        6         2          2          3
                    vv
clus                 STAGE IV
  17P LOSS MUTATED          1
  17P LOSS WILD-TYPE        0
D35V7, multiclass

Clustering(36) Variable = 18p loss mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  1
  18P LOSS WILD-TYPE  6 15
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 21 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                 15 
$`18P LOSS MUTATED`
TCGA-EE-A2GR TCGA-EE-A2MS TCGA-EE-A3AE TCGA-FS-A1ZA 
       14.30       136.44        26.73        27.68 

$`18P LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO 
        2.56        18.58        25.87        24.43        43.23       101.95 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP 
      204.62        96.23        41.59        26.37        20.91        74.73 
TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       27.02         0.20        10.09 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              14.3                0.2 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            136.44             204.62 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            27.205             27.020 
[1] "14.3 - 136.4 (27.2)" "0.2 - 204.6 (27.0)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18P LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18P LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D36V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18P LOSS MUTATED                    1
  18P LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          1
  18P LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                     2
  18P LOSS WILD-TYPE                  11
D36V3, multiclass
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      11
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    2
  18P LOSS WILD-TYPE    6   15
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                2                  6
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  18P LOSS MUTATED    3   0   1  0
  18P LOSS WILD-TYPE 13   3   1  2
D36V5, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                 3                 13
  N1B                0                  3
  N2C                1                  1
  N3                 0                  2
D36V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  18P LOSS MUTATED          1        0        2         0          1          0
  18P LOSS WILD-TYPE        2        1        4         3          2          4
                    vv
clus                 STAGE IV
  18P LOSS MUTATED          0
  18P LOSS WILD-TYPE        1
D36V7, multiclass

Clustering(37) Variable = 18q loss mutation analysis
D37V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    2  1
  18Q LOSS WILD-TYPE  7 15
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 22 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                 15 
$`18Q LOSS MUTATED`
TCGA-EE-A29V TCGA-EE-A2GR TCGA-EE-A3AE 
       25.87        14.30        26.73 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       48.76        20.38        68.09        29.82        33.73        14.70 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MI 
        2.56        18.58        24.43        43.23       101.95       204.62 
TCGA-EE-A2MJ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZA 
       96.23       136.44        41.59        26.37        20.91        27.68 
TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 TCGA-GN-A266 
       74.73        27.02         0.20        10.09 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              14.3                0.2 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             26.73             204.62 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             25.87              28.75 
[1] "14.3 - 26.7 (25.9)" "0.2 - 204.6 (28.8)"
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
"18Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 DISTANT METASTASIS
  18Q LOSS MUTATED                    1
  18Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          1
  18Q LOSS WILD-TYPE                                                                                        4
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                     1
  18Q LOSS WILD-TYPE                  12
D37V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  4
  REGIONAL LYMPH NODE                                                                                      12
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    2
  18Q LOSS WILD-TYPE    7   15
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                1                  7
  MALE                  2                 15
                    vv
clus                 N0 N1B N2C N3
  18Q LOSS MUTATED    2   1   0  0
  18Q LOSS WILD-TYPE 14   2   2  2
D37V5, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                 2                 14
  N1B                1                  2
  N2C                0                  2
  N3                 0                  2
D37V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED          1        0        1         0          0          1
  18Q LOSS WILD-TYPE        2        1        5         3          3          3
                    vv
clus                 STAGE IV
  18Q LOSS MUTATED          0
  18Q LOSS WILD-TYPE        1
D37V7, multiclass

Clustering(38) Variable = 21q loss mutation analysis
D38V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    4  3
  21Q LOSS WILD-TYPE  5 13
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                 18 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 13 
$`21Q LOSS MUTATED`
TCGA-EE-A181 TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GO TCGA-EE-A2MS TCGA-FS-A1ZA 
       33.73        24.43        43.23       101.95       136.44        27.68 
TCGA-GN-A266 
       10.09 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A2JF TCGA-DA-A1I0 TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A29L 
       48.76        20.38        68.09        29.82        14.70         2.56 
TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A2GR TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MT 
       18.58        25.87        14.30       204.62        96.23        41.59 
TCGA-EE-A3AE TCGA-ER-A19F TCGA-FS-A1Z3 TCGA-FS-A1ZP TCGA-FS-A1ZZ TCGA-FW-A3I3 
       26.73        26.37        20.91        74.73        27.02         0.20 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             10.09               0.20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            136.44             204.62 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             33.73              26.55 
[1] "10.1 - 136.4 (33.7)" "0.2 - 204.6 (26.6)" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "21Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "21Q LOSS MUTATED" 
        TCGA-D3-A2JF         TCGA-DA-A1I0         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A17X         TCGA-EE-A181         TCGA-EE-A182 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2GC         TCGA-EE-A2GO 
  "21Q LOSS MUTATED"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-EE-A2GR         TCGA-EE-A2MI         TCGA-EE-A2MJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2MS         TCGA-EE-A2MT         TCGA-EE-A3AE 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19F         TCGA-FS-A1Z3         TCGA-FS-A1ZA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-FS-A1ZP         TCGA-FS-A1ZZ         TCGA-FW-A3I3 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266 
  "21Q LOSS MUTATED" 
[1] "hr=" "2.2"
D38V2, continuous
                    vv
clus                 DISTANT METASTASIS
  21Q LOSS MUTATED                    1
  21Q LOSS WILD-TYPE                  6
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          2
  21Q LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                     4
  21Q LOSS WILD-TYPE                   9
D38V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                       9
D38V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    4
  21Q LOSS WILD-TYPE    5   13
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                3                  5
  MALE                  4                 13
                    vv
clus                 N0 N1B N2C N3
  21Q LOSS MUTATED    4   1   1  0
  21Q LOSS WILD-TYPE 12   2   1  2
D38V5, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                 4                 12
  N1B                1                  2
  N2C                1                  1
  N3                 0                  2
D38V6, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE II STAGE IIB STAGE IIIB STAGE IIIC
  21Q LOSS MUTATED          0        0        3         1          2          0
  21Q LOSS WILD-TYPE        3        1        3         2          1          4
                    vv
clus                 STAGE IV
  21Q LOSS MUTATED          0
  21Q LOSS WILD-TYPE        1
D38V7, 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")
