
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-BRAF_Hotspot_Mutants/3164349/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215664/SKCM-BRAF_Hotspot_Mutants.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-BRAF_Hotspot_Mutants", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"                           "-oT=SKCM-BRAF_Hotspot_Mutants"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=67, in cluster file=99, common to both=67
[1] "Reduce the number of clustering variables from 80 to 70."
[1] 70 67
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                64 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                64 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                51 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                51 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                61 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                61 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                61 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                61 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                63 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                63 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                62 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                62 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                62 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                62 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                62 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                62 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                60 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                60 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15                52 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15                52 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                62 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                62 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               40                27 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               40                27 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                23 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               44                23 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                55 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                55 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23                44 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               23                44 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 62 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 62 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 64 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 64 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 56 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 56 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 62 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 62 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 59 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 59 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 62 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 62 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 56 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 56 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 62 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 62 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 61 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 61 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 60 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 7                 60 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 61 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 61 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 57 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 57 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 63 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 63 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 61 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 61 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 60 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 60 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 43 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                24                 43 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                28                 39 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                28                 39 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 63 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 63 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 50 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                17                 50 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                61 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                63 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                63 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                60 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                60 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                60 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                7                60 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                58 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                58 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                58 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                58 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                63 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                63 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                63 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                58 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                9                58 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                47 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                47 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                61 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                61 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31                36 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31                36 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                60 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                60 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                29 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               38                29 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                38 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29                38 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 31 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 31 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 22 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                45                 22 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 54 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                13                 54 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 52 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 52 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 64 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 64 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 63 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 63 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 57 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                10                 57 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 49 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 49 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 61 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 61 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 62 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 62 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 57 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 57 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 55 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 55 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 62 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 62 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 51 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 51 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 50 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                17                 50 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 61 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 61 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 59 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 59 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 64 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 64 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 59 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 59 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 63 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 63 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                63 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                63 
[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 67 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
          NA           NA         3004           NA           NA           NA 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A1JX 
          NA           NA           NA           NA           NA           NA 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
          NA         1555           NA           NA           NA         1354 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        1116           NA          534          451           NA         1097 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
         156           NA           NA         1155         1175          134 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GE 
         825          366          197          272           NA           NA 
TCGA-EE-A2GH TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19J 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19O TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-GN-A262 
          NA           NA           NA           NA           NA          756 
TCGA-GN-A265 
        2577 
Variable 1:'AGE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=36,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=12,	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"                  "DISTANT.METASTASIS"     
[5] "LYMPH.NODE.METASTASIS"   "TUMOR.STAGECODE"        
[7] "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T0  T1 T1A T1B  T2 T2A T2B  T3 T3A T3B  T4 T4A T4B TIS  TX 
  2   1   5   1  11   6   2   2   7   3   1   2  10   1   7 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 67 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=44, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=9, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=12, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    2  0
  1P GAIN WILD-TYPE 15 19
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                34 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                19 
$`1P GAIN MUTATED`
TCGA-EE-A29E TCGA-EE-A29M 
       38.63        27.12 

$`1P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        7.96        37.97         4.41        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            27.12              4.18 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            38.63             98.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           32.875            14.255 
[1] "27.1 - 38.6 (32.9)" "4.2 - 98.8 (14.3)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                34 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29H        TCGA-EE-A29P 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-ER-A19J        TCGA-FS-A1ZR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                    0             1
  1P GAIN WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          0
  1P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                     2
  1P GAIN WILD-TYPE                  46
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     46
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    1
  1P GAIN WILD-TYPE   20   44
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 1                44
                   vv
clus                M0 M1 M1A M1B M1C
  1P GAIN MUTATED    3  0   0   0   0
  1P GAIN WILD-TYPE 53  1   1   1   2
D1V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1P GAIN MUTATED    2  0   0   1   0   0   0  0  0
  1P GAIN WILD-TYPE 31  1   2   6   1   5   3  7  2
D1V6, multiclass
D1V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P GAIN MUTATED             0       0        0        2        0         0
  1P GAIN WILD-TYPE           2      10        2        3        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P GAIN MUTATED           0         0          0          1          0
  1P GAIN WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  1P GAIN MUTATED          0
  1P GAIN WILD-TYPE        3
D1V8, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    5  4
  1Q GAIN WILD-TYPE 12 15
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                27 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                15 
$`1Q GAIN MUTATED`
TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-EE-A20B 
       11.41        13.32         9.30         9.99        44.52        36.07 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A2A6 
       38.63        27.12         8.94 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JK 
       32.55        70.16        98.76        22.55        21.14         6.35 
TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       15.25        35.80        51.12        10.03        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       25.15        17.56        14.83        12.20         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J 
        7.96        37.97         4.41        12.03         6.48         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             8.94              4.18 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            44.52             98.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            13.32             15.25 
[1] "8.9 - 44.5 (13.3)" "4.2 - 98.8 (15.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                    3             1
  1Q GAIN WILD-TYPE                  3             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                          3
  1Q GAIN WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                     9
  1Q GAIN WILD-TYPE                  39
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     39
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   10
  1Q GAIN WILD-TYPE   16   35
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                16
  MALE                10                35
                   vv
clus                M0 M1 M1A M1B M1C
  1Q GAIN MUTATED   13  0   0   0   1
  1Q GAIN WILD-TYPE 43  1   1   1   1
D2V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1Q GAIN MUTATED    9  0   0   3   0   1   1  0  0
  1Q GAIN WILD-TYPE 24  1   2   4   1   4   2  7  2
D2V6, multiclass
D2V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q GAIN MUTATED             1       1        1        2        2         0
  1Q GAIN WILD-TYPE           1       9        1        3        6         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q GAIN MUTATED           1         2          0          2          1
  1Q GAIN WILD-TYPE         1         3          2          5          8
                   vv
clus                STAGE IV
  1Q GAIN MUTATED          1
  1Q GAIN WILD-TYPE        2
D2V8, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    0  5
  2P GAIN WILD-TYPE 17 14
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                31 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                14 
$`2P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A20H TCGA-EE-A29A 
       70.16        22.55        11.41         8.81         7.96 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       32.55        98.76        21.14         6.35        15.25        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       44.52        36.69        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       36.07         5.13        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             7.96              4.18 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            70.16             98.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            11.41             15.25 
[1] "8.0 - 70.2 (11.4)" "4.2 - 98.8 (15.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    2             0
  2P GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P GAIN MUTATED                                                                                          1
  2P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                     3
  2P GAIN WILD-TYPE                  45
D3V3, multiclass
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0    6
  2P GAIN WILD-TYPE   22   39
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 6                39
                   vv
clus                M0 M1 M1A M1B M1C
  2P GAIN MUTATED    6  0   0   0   0
  2P GAIN WILD-TYPE 50  1   1   1   2
D3V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2P GAIN MUTATED    2  0   1   2   1   0   0  0  0
  2P GAIN WILD-TYPE 31  1   1   5   0   5   3  7  2
D3V6, multiclass
D3V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P GAIN MUTATED             0       1        0        0        0         1
  2P GAIN WILD-TYPE           2       9        2        5        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P GAIN MUTATED           0         1          1          1          1
  2P GAIN WILD-TYPE         2         4          1          6          8
                   vv
clus                STAGE IV
  2P GAIN MUTATED          0
  2P GAIN WILD-TYPE        3
D3V8, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    0  5
  2Q GAIN WILD-TYPE 17 14
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                31 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                14 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-EE-A20H TCGA-EE-A29A 
       70.16        22.55        11.41         8.81         7.96 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       32.55        98.76        21.14         6.35        15.25        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       44.52        36.69        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
       36.07         5.13        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             7.96              4.18 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            70.16             98.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            11.41             15.25 
[1] "8.0 - 70.2 (11.4)" "4.2 - 98.8 (15.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    2             0
  2Q GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q GAIN MUTATED                                                                                          1
  2Q GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                     3
  2Q GAIN WILD-TYPE                  45
D4V3, multiclass
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    6
  2Q GAIN WILD-TYPE   22   39
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 6                39
                   vv
clus                M0 M1 M1A M1B M1C
  2Q GAIN MUTATED    6  0   0   0   0
  2Q GAIN WILD-TYPE 50  1   1   1   2
D4V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2Q GAIN MUTATED    2  0   1   2   1   0   0  0  0
  2Q GAIN WILD-TYPE 31  1   1   5   0   5   3  7  2
D4V6, multiclass
D4V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q GAIN MUTATED             0       1        0        0        0         1
  2Q GAIN WILD-TYPE           2       9        2        5        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q GAIN MUTATED           0         1          1          1          1
  2Q GAIN WILD-TYPE         2         4          1          6          8
                   vv
clus                STAGE IV
  2Q GAIN MUTATED          0
  2Q GAIN WILD-TYPE        3
D4V8, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  1
  3P GAIN WILD-TYPE 14 18
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                32 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                18 
$`3P GAIN MUTATED`
TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T 
       17.56         8.81        27.12         6.48 

$`3P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       14.83        12.20        36.07         5.13         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       38.63         4.41        12.03         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             6.48              4.18 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            27.12             98.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           13.185            15.040 
[1] "6.5 - 27.1 (13.2)" "4.2 - 98.8 (15.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                    1             1
  3P GAIN WILD-TYPE                  5             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          0
  3P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     2
  3P GAIN WILD-TYPE                  46
D5V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     46
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    2
  3P GAIN WILD-TYPE   20   43
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 2                43
                   vv
clus                M0 M1 M1A M1B M1C
  3P GAIN MUTATED    4  0   0   0   0
  3P GAIN WILD-TYPE 52  1   1   1   2
D5V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3P GAIN MUTATED    2  0   0   0   0   0   0  1  1
  3P GAIN WILD-TYPE 31  1   2   7   1   5   3  6  1
D5V6, multiclass
D5V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P GAIN MUTATED             0       1        0        1        0         0
  3P GAIN WILD-TYPE           2       9        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P GAIN MUTATED           0         0          0          0          1
  3P GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  3P GAIN MUTATED          0
  3P GAIN WILD-TYPE        3
D5V8, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    4  1
  3Q GAIN WILD-TYPE 13 18
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                31 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                18 
$`3Q GAIN MUTATED`
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29T 
       17.56         5.13         8.81        27.12         6.48 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       14.83        12.20        36.07         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
        4.41        12.03         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5.13              4.18 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            27.12             98.76 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             8.81             15.25 
[1] "5.1 - 27.1 (8.8)"  "4.2 - 98.8 (15.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D6V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                    1             1
  3Q GAIN WILD-TYPE                  5             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          0
  3Q GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     3
  3Q GAIN WILD-TYPE                  45
D6V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     45
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    3
  3Q GAIN WILD-TYPE   20   42
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  3Q GAIN MUTATED    5  0   0   0   0
  3Q GAIN WILD-TYPE 51  1   1   1   2
D6V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3Q GAIN MUTATED    3  0   0   0   0   0   0  1  1
  3Q GAIN WILD-TYPE 30  1   2   7   1   5   3  6  1
D6V6, multiclass
D6V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q GAIN MUTATED             0       1        0        1        1         0
  3Q GAIN WILD-TYPE           2       9        2        4        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q GAIN MUTATED           0         0          0          0          1
  3Q GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  3Q GAIN MUTATED          0
  3Q GAIN WILD-TYPE        3
D6V8, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 15 18
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                33 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                18 
$`4P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F5 TCGA-EE-A29P 
       13.32        17.56        12.03 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 
       13.68         9.99        44.52        36.69        25.15        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
       38.63         4.41        27.12         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            12.03              4.18 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            17.56             98.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            13.32             15.25 
[1] "12.0 - 17.6 (13.3)" "4.2 - 98.8 (15.2)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    0             0
  4P GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          1
  4P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                     4
  4P GAIN WILD-TYPE                  44
D7V3, multiclass
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     44
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    3
  4P GAIN WILD-TYPE   20   42
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4P GAIN MUTATED    5  0   0   0   0
  4P GAIN WILD-TYPE 51  1   1   1   2
D7V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4P GAIN MUTATED    1  0   1   1   0   0   1  1  0
  4P GAIN WILD-TYPE 32  1   1   6   1   5   2  6  2
D7V6, multiclass
D7V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P GAIN MUTATED             0       0        0        0        0         0
  4P GAIN WILD-TYPE           2      10        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P GAIN MUTATED           1         2          1          0          1
  4P GAIN WILD-TYPE         1         3          1          7          8
                   vv
clus                STAGE IV
  4P GAIN MUTATED          0
  4P GAIN WILD-TYPE        3
D7V8, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    2  1
  4Q GAIN WILD-TYPE 15 18
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                33 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                18 
$`4Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F5 TCGA-EE-A29P 
       13.32        17.56        12.03 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 
       13.68         9.99        44.52        36.69        25.15        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
       38.63         4.41        27.12         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            12.03              4.18 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            17.56             98.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            13.32             15.25 
[1] "12.0 - 17.6 (13.3)" "4.2 - 98.8 (15.2)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    0             0
  4Q GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          0
  4Q GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                     5
  4Q GAIN WILD-TYPE                  43
D8V3, multiclass
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     43
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    3
  4Q GAIN WILD-TYPE   20   42
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4Q GAIN MUTATED    4  0   0   0   0
  4Q GAIN WILD-TYPE 52  1   1   1   2
D8V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4Q GAIN MUTATED    1  0   1   1   0   0   0  1  0
  4Q GAIN WILD-TYPE 32  1   1   6   1   5   3  6  2
D8V6, multiclass
D8V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q GAIN MUTATED             0       0        0        0        0         0
  4Q GAIN WILD-TYPE           2      10        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q GAIN MUTATED           1         1          1          0          1
  4Q GAIN WILD-TYPE         1         4          1          7          8
                   vv
clus                STAGE IV
  4Q GAIN MUTATED          0
  4Q GAIN WILD-TYPE        3
D8V8, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    1  2
  5P GAIN WILD-TYPE 16 17
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                17 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A20H TCGA-EE-A29T 
       32.55         8.81         6.48 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       14.83        12.20        36.07         5.13         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J 
       38.63         4.41        27.12        12.03         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             6.48              4.18 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            32.55             98.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             8.81             15.25 
[1] "6.5 - 32.5 (8.8)"  "4.2 - 98.8 (15.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                    1             0
  5P GAIN WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P GAIN MUTATED                                                                                          0
  5P GAIN WILD-TYPE                                                                                       12
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                     6
  5P GAIN WILD-TYPE                  42
D9V3, multiclass
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                12
  REGIONAL LYMPH NODE                                                                                     42
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    5
  5P GAIN WILD-TYPE   20   40
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  5P GAIN MUTATED    6  0   0   1   0
  5P GAIN WILD-TYPE 50  1   1   0   2
D9V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5P GAIN MUTATED    4  0   0   1   0   0   0  1  1
  5P GAIN WILD-TYPE 29  1   2   6   1   5   3  6  1
D9V6, multiclass
D9V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P GAIN MUTATED             1       3        0        0        0         0
  5P GAIN WILD-TYPE           1       7        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P GAIN MUTATED           0         0          0          1          0
  5P GAIN WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  5P GAIN MUTATED          0
  5P GAIN WILD-TYPE        3
D9V8, multiclass

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    2  5
  6P GAIN WILD-TYPE 15 14
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                14 
$`6P GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-EE-A20H 
       98.76        21.14        15.25        10.03        13.68         8.81 
TCGA-EE-A29P 
       12.03 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
       32.55        70.16        22.55        11.41         6.35        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
        9.30        35.80        51.12         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       25.15        17.56        14.83        12.20        36.07         5.13 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T 
        7.96        37.97        38.63         4.41        27.12         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.94         4.18         8.81        24.85        84.72 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             8.81              4.18 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            98.76             84.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            13.68             17.56 
[1] "8.8 - 98.8 (13.7)" "4.2 - 84.7 (17.6)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D10V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                    2             0
  6P GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          1
  6P GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    12
  6P GAIN WILD-TYPE                  36
D10V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     36
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    9
  6P GAIN WILD-TYPE   16   36
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               6                16
  MALE                 9                36
                   vv
clus                M0 M1 M1A M1B M1C
  6P GAIN MUTATED   12  0   1   0   0
  6P GAIN WILD-TYPE 44  1   0   1   2
D10V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6P GAIN MUTATED    9  0   0   1   0   1   0  2  0
  6P GAIN WILD-TYPE 24  1   2   6   1   4   3  5  2
D10V6, multiclass
D10V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             1       3        0        2        1         1
  6P GAIN WILD-TYPE           1       7        2        3        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P GAIN MUTATED           1         0          0          1          3
  6P GAIN WILD-TYPE         1         5          2          6          6
                   vv
clus                STAGE IV
  6P GAIN MUTATED          0
  6P GAIN WILD-TYPE        3
D10V8, multiclass

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    1  1
  6Q GAIN WILD-TYPE 16 18
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                34 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                18 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-DA-A1I0 
       98.76        10.03 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       15.25        13.32         9.30        35.80        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            10.03              4.18 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            98.76             84.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           54.395            15.040 
[1] "10.0 - 98.8 (54.4)" "4.2 - 84.7 (15.0)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                34 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q9        TCGA-D3-A2J9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CE 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-ER-A19J        TCGA-FS-A1ZR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    1             0
  6Q GAIN WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q GAIN MUTATED                                                                                          1
  6Q GAIN WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                     3
  6Q GAIN WILD-TYPE                  45
D11V3, multiclass
                                                                                          clus
vv                                                                                         6Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    4
  6Q GAIN WILD-TYPE   21   41
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1                21
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  6Q GAIN MUTATED    4  0   1   0   0
  6Q GAIN WILD-TYPE 52  1   0   1   2
D11V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6Q GAIN MUTATED    4  0   0   0   0   0   0  1  0
  6Q GAIN WILD-TYPE 29  1   2   7   1   5   3  6  2
D11V6, multiclass
D11V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q GAIN MUTATED             1       1        0        1        0         1
  6Q GAIN WILD-TYPE           1       9        2        4        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q GAIN MUTATED           0         0          0          0          1
  6Q GAIN WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  6Q GAIN MUTATED          0
  6Q GAIN WILD-TYPE        3
D11V8, multiclass

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    8 13
  7P GAIN WILD-TYPE  9  6
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               13                 6 
$`7P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO TCGA-DA-A1HY 
       32.55        70.16        22.55        11.41         9.30        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T 
        8.81         7.96        37.97        38.63        12.03         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        8.94         4.18         8.81 

$`7P GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HW 
       98.76        21.14         6.35        15.25        13.32        35.80 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H 
       17.56        14.83        12.20        36.07         5.13         4.41 
TCGA-EE-A29M TCGA-GN-A262 TCGA-GN-A265 
       27.12        24.85        84.72 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.18              4.41 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            70.16             98.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            12.03             17.56 
[1] "4.2 - 70.2 (12.0)" "4.4 - 98.8 (17.6)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D12V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                    4             0
  7P GAIN WILD-TYPE                  2             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                          9
  7P GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                    27
  7P GAIN WILD-TYPE                  21
D12V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                     4
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   27
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     21
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9   31
  7P GAIN WILD-TYPE   13   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               9                13
  MALE                31                14
                   vv
clus                M0 M1 M1A M1B M1C
  7P GAIN MUTATED   33  1   1   0   2
  7P GAIN WILD-TYPE 23  0   0   1   0
D12V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  7P GAIN MUTATED   17  0   2   5   1   3   3  4  2
  7P GAIN WILD-TYPE 16  1   0   2   0   2   0  3  0
D12V6, multiclass
D12V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             2       5        1        1        5         1
  7P GAIN WILD-TYPE           0       5        1        4        3         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7P GAIN MUTATED           1         3          2          5          6
  7P GAIN WILD-TYPE         1         2          0          2          3
                   vv
clus                STAGE IV
  7P GAIN MUTATED          3
  7P GAIN WILD-TYPE        0
D12V8, multiclass

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   10 14
  7Q GAIN WILD-TYPE  7  5
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                12 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               14                 5 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO TCGA-DA-A1HY 
       32.55        70.16        22.55        11.41         9.30        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       17.56        14.83        12.20         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       38.63        12.03         6.48         8.94         4.18         8.81 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HW 
       98.76        21.14         6.35        15.25        13.32        35.80 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-GN-A262 TCGA-GN-A265 
       36.07         5.13         4.41        27.12        24.85        84.72 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.18              4.41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.16             98.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           12.940            22.995 
[1] "4.2 - 70.2 (12.9)" "4.4 - 98.8 (23.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D13V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                    5             0
  7Q GAIN WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                          9
  7Q GAIN WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                    30
  7Q GAIN WILD-TYPE                  18
D13V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   30
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     18
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     10   34
  7Q GAIN WILD-TYPE   12   11
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              10                12
  MALE                34                11
                   vv
clus                M0 M1 M1A M1B M1C
  7Q GAIN MUTATED   38  1   1   0   2
  7Q GAIN WILD-TYPE 18  0   0   1   0
D13V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  7Q GAIN MUTATED   20  0   2   5   1   4   3  5  2
  7Q GAIN WILD-TYPE 13  1   0   2   0   1   0  2  0
D13V6, multiclass
D13V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             2       6        1        1        6         1
  7Q GAIN WILD-TYPE           0       4        1        4        2         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  7Q GAIN MUTATED           2         3          2          6          7
  7Q GAIN WILD-TYPE         0         2          0          1          2
                   vv
clus                STAGE IV
  7Q GAIN MUTATED          3
  7Q GAIN WILD-TYPE        0
D13V8, multiclass

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    2  6
  8P GAIN WILD-TYPE 15 13
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                28 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                13 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 
       70.16        13.32        51.12        13.68         9.99        17.56 
TCGA-ER-A19J TCGA-FS-A1ZR 
        4.18         8.81 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
       15.25         9.30        35.80        10.03        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       25.15        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
        7.96        37.97        38.63         4.41        27.12        12.03 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94        24.85        84.72 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             4.18              4.41 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.16             98.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           13.500            18.195 
[1] "4.2 - 70.2 (13.5)" "4.4 - 98.8 (18.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D14V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                    0             0
  8P GAIN WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                          3
  8P GAIN WILD-TYPE                                                                                        9
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                     9
  8P GAIN WILD-TYPE                  39
D14V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 9
  REGIONAL LYMPH NODE                                                                                     39
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   11
  8P GAIN WILD-TYPE   21   34
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                21
  MALE                11                34
                   vv
clus                M0 M1 M1A M1B M1C
  8P GAIN MUTATED   10  1   0   0   0
  8P GAIN WILD-TYPE 46  0   1   1   2
D14V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8P GAIN MUTATED    3  0   0   3   0   2   0  3  0
  8P GAIN WILD-TYPE 30  1   2   4   1   3   3  4  2
D14V6, multiclass
D14V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P GAIN MUTATED             0       1        0        0        1         1
  8P GAIN WILD-TYPE           2       9        2        5        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P GAIN MUTATED           0         2          0          1          4
  8P GAIN WILD-TYPE         2         3          2          6          5
                   vv
clus                STAGE IV
  8P GAIN MUTATED          1
  8P GAIN WILD-TYPE        2
D14V8, multiclass

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    4  9
  8Q GAIN WILD-TYPE 13 10
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               13                23 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                10 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 
       70.16        22.55        13.32         9.30        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A29E TCGA-EE-A29T TCGA-ER-A19J 
       13.68         9.99        17.56        38.63         6.48         4.18 
TCGA-FS-A1ZR 
        8.81 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       32.55        98.76        21.14        11.41         6.35        15.25 
TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
       35.80        44.52        36.69        25.15        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
       36.07         5.13         8.81         7.96        37.97         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-GN-A262 TCGA-GN-A265 
       27.12        12.03         8.94        24.85        84.72 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             4.18              4.41 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            70.16             98.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.32             21.14 
[1] "4.2 - 70.2 (13.3)" "4.4 - 98.8 (21.1)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D15V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                    2             0
  8Q GAIN WILD-TYPE                  4             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                          5
  8Q GAIN WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    16
  8Q GAIN WILD-TYPE                  32
D15V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   16
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     32
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   19
  8Q GAIN WILD-TYPE   18   26
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               4                18
  MALE                19                26
                   vv
clus                M0 M1 M1A M1B M1C
  8Q GAIN MUTATED   19  1   1   0   0
  8Q GAIN WILD-TYPE 37  0   0   1   2
D15V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8Q GAIN MUTATED    8  0   0   4   1   2   1  4  1
  8Q GAIN WILD-TYPE 25  1   2   3   0   3   2  3  1
D15V6, multiclass
D15V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q GAIN MUTATED             1       2        0        1        2         2
  8Q GAIN WILD-TYPE           1       8        2        4        6         1
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8Q GAIN MUTATED           0         3          0          3          5
  8Q GAIN WILD-TYPE         2         2          2          4          4
                   vv
clus                STAGE IV
  8Q GAIN MUTATED          1
  8Q GAIN WILD-TYPE        2
D15V8, multiclass

Clustering(16) Variable = 11p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    1  1
  11P GAIN WILD-TYPE 16 18
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 34 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 18 
$`11P GAIN MUTATED`
TCGA-D3-A3CE TCGA-EE-A29T 
       13.32         6.48 

$`11P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 
       37.97        38.63         4.41        27.12        12.03         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.48               4.18 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.32              98.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             9.900             16.405 
[1] "6.5 - 13.3 (9.9)"  "4.2 - 98.8 (16.4)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 34 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3MO 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A2A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-FS-A1ZR         TCGA-GN-A262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A265 
"11P GAIN WILD-TYPE" 
D16V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    0             0
  11P GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P GAIN MUTATED                                                                                          0
  11P GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                     5
  11P GAIN WILD-TYPE                  43
D16V3, multiclass
                                                                                          clus
vv                                                                                         11P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      43
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    3
  11P GAIN WILD-TYPE   20   42
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  11P GAIN MUTATED    5  0   0   0   0
  11P GAIN WILD-TYPE 51  1   1   1   2
D16V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11P GAIN MUTATED    2  0   1   1   0   0   0  0  1
  11P GAIN WILD-TYPE 31  1   1   6   1   5   3  7  1
D16V6, multiclass
D16V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P GAIN MUTATED             0       0        0        0        1         1
  11P GAIN WILD-TYPE           2      10        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P GAIN MUTATED           0         1          1          0          0
  11P GAIN WILD-TYPE         2         4          1          7          9
                    vv
clus                 STAGE IV
  11P GAIN MUTATED          0
  11P GAIN WILD-TYPE        3
D16V8, multiclass

Clustering(17) Variable = 11q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    0  1
  11Q GAIN WILD-TYPE 17 18
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 35 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 18 
$`11Q GAIN MUTATED`
TCGA-D3-A3CE 
       13.32 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       37.97        38.63         4.41        27.12        12.03         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.94         4.18         8.81        24.85        84.72 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.32               4.18 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.32              98.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.32              15.25 
[1] "13.3 - 13.3 (13.3)" "4.2 - 98.8 (15.2)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 1                 35 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3MO 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19J         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
D17V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    0             0
  11Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q GAIN MUTATED                                                                                          0
  11Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                     3
  11Q GAIN WILD-TYPE                  45
D17V3, multiclass
                                                                                          clus
vv                                                                                         11Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      45
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE   21   43
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  11Q GAIN MUTATED    3  0   0   0   0
  11Q GAIN WILD-TYPE 53  1   1   1   2
D17V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11Q GAIN MUTATED    2  0   0   1   0   0   0  0  0
  11Q GAIN WILD-TYPE 31  1   2   6   1   5   3  7  2
D17V6, multiclass
D17V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q GAIN MUTATED             0       0        0        0        1         1
  11Q GAIN WILD-TYPE           2      10        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q GAIN MUTATED           0         1          0          0          0
  11Q GAIN WILD-TYPE         2         4          2          7          9
                    vv
clus                 STAGE IV
  11Q GAIN MUTATED          0
  11Q GAIN WILD-TYPE        3
D17V8, multiclass

Clustering(18) Variable = 12p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    3  5
  12P GAIN WILD-TYPE 14 14
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 28 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 14 
$`12P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H 
       70.16        22.55        13.32        36.69        17.56         8.81 
TCGA-EE-A2A6 TCGA-ER-A19J 
        8.94         4.18 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       32.55        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        9.30        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       44.52        25.15        14.83        12.20        36.07         5.13 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
        7.96        37.97        38.63         4.41        27.12        12.03 
TCGA-EE-A29T TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.81        24.85        84.72 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.18               4.41 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             70.16              98.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             15.44              15.04 
[1] "4.2 - 70.2 (15.4)" "4.4 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D18V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    1             0
  12P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          3
  12P GAIN WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                     7
  12P GAIN WILD-TYPE                  41
D18V3, multiclass
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      41
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1   10
  12P GAIN WILD-TYPE   21   35
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  12P GAIN MUTATED   10  1   0   0   0
  12P GAIN WILD-TYPE 46  0   1   1   2
D18V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12P GAIN MUTATED    3  0   1   2   1   1   1  2  0
  12P GAIN WILD-TYPE 30  1   1   5   0   4   2  5  2
D18V6, multiclass
D18V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P GAIN MUTATED             0       2        1        0        0         0
  12P GAIN WILD-TYPE           2       8        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12P GAIN MUTATED           0         3          1          2          1
  12P GAIN WILD-TYPE         2         2          1          5          8
                    vv
clus                 STAGE IV
  12P GAIN MUTATED          1
  12P GAIN WILD-TYPE        2
D18V8, multiclass

Clustering(19) Variable = 12q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  2
  12Q GAIN WILD-TYPE 15 17
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 32 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 17 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-DA-A3F5 TCGA-EE-A2A6 
       70.16        22.55        17.56         8.94 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       32.55        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       13.32         9.30        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 
        9.99        44.52        36.69        25.15        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR 
        4.41        27.12        12.03         6.48         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              8.94               4.18 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16              98.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            20.055             14.255 
[1] "8.9 - 70.2 (20.1)" "4.2 - 98.8 (14.3)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    0             0
  12Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q GAIN MUTATED                                                                                          1
  12Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                     4
  12Q GAIN WILD-TYPE                  44
D19V3, multiclass
                                                                                          clus
vv                                                                                         12Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    5
  12Q GAIN WILD-TYPE   22   40
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  12Q GAIN MUTATED    5  0   0   0   0
  12Q GAIN WILD-TYPE 51  1   1   1   2
D19V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12Q GAIN MUTATED    1  0   1   1   1   0   0  1  0
  12Q GAIN WILD-TYPE 32  1   1   6   0   5   3  6  2
D19V6, multiclass
D19V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q GAIN MUTATED             0       0        1        0        0         0
  12Q GAIN WILD-TYPE           2      10        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN MUTATED           0         1          1          1          1
  12Q GAIN WILD-TYPE         2         4          1          6          8
                    vv
clus                 STAGE IV
  12Q GAIN MUTATED          0
  12Q GAIN WILD-TYPE        3
D19V8, multiclass

Clustering(20) Variable = 13q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    2  3
  13Q GAIN WILD-TYPE 15 16
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 31 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 16 
$`13Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29P 
       13.32        36.69         8.81         7.96        12.03 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       13.68         9.99        44.52        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       12.20        36.07         5.13        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       27.12         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              7.96               4.18 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             36.69              98.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.03              17.56 
[1] "8.0 - 36.7 (12.0)" "4.2 - 98.8 (17.6)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                    2             0
  13Q GAIN WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q GAIN MUTATED                                                                                          1
  13Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                     5
  13Q GAIN WILD-TYPE                  43
D20V3, multiclass
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    5
  13Q GAIN WILD-TYPE   19   40
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  13Q GAIN MUTATED    7  0   0   0   0
  13Q GAIN WILD-TYPE 49  1   1   1   2
D20V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  13Q GAIN MUTATED    2  0   2   2   0   1   0  0  0
  13Q GAIN WILD-TYPE 31  1   0   5   1   4   3  7  2
D20V6, multiclass
D20V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       1        0        0        0         0
  13Q GAIN WILD-TYPE           2       9        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  13Q GAIN MUTATED           1         1          2          1          1
  13Q GAIN WILD-TYPE         1         4          0          6          8
                    vv
clus                 STAGE IV
  13Q GAIN MUTATED          0
  13Q GAIN WILD-TYPE        3
D20V8, multiclass

Clustering(21) Variable = 14q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    1  3
  14Q GAIN WILD-TYPE 16 16
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                 32 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 3                 16 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A20H 
       22.55        13.68        36.69         8.81 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
        9.99        44.52        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              8.81               4.18 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             36.69              98.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            18.115             15.040 
[1] "8.8 - 36.7 (18.1)" "4.2 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D21V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    1             0
  14Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q GAIN MUTATED                                                                                          1
  14Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                     3
  14Q GAIN WILD-TYPE                  45
D21V3, multiclass
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           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                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0    5
  14Q GAIN WILD-TYPE   22   40
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  14Q GAIN MUTATED    5  0   0   0   0
  14Q GAIN WILD-TYPE 51  1   1   1   2
D21V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  14Q GAIN MUTATED    2  0   0   0   1   2   0  0  0
  14Q GAIN WILD-TYPE 31  1   2   7   0   3   3  7  2
D21V6, multiclass
D21V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q GAIN MUTATED             0       2        0        0        0         0
  14Q GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q GAIN MUTATED           0         0          0          2          1
  14Q GAIN WILD-TYPE         2         5          2          5          8
                    vv
clus                 STAGE IV
  14Q GAIN MUTATED          0
  14Q GAIN WILD-TYPE        3
D21V8, multiclass

Clustering(22) Variable = 15q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  7
  15Q GAIN WILD-TYPE 15 12
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                 27 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 7                 12 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1I7 
       32.55        22.55        21.14        13.32        35.80        36.69 
TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20H 
       17.56        12.20         8.81 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO 
       70.16        98.76        11.41         6.35        15.25         9.30 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       51.12        10.03        13.68         9.99        44.52        25.15 
TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       14.83        36.07         5.13         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.81               4.18 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             36.69              98.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             21.14              13.68 
[1] "8.8 - 36.7 (21.1)" "4.2 - 98.8 (13.7)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "15Q GAIN MUTATED"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                    1             0
  15Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          1
  15Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                     9
  15Q GAIN WILD-TYPE                  39
D22V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      39
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    9
  15Q GAIN WILD-TYPE   20   36
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  9                 36
                    vv
clus                 M0 M1 M1A M1B M1C
  15Q GAIN MUTATED   11  0   0   0   0
  15Q GAIN WILD-TYPE 45  1   1   1   2
D22V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  15Q GAIN MUTATED    5  0   0   2   1   1   0  2  0
  15Q GAIN WILD-TYPE 28  1   2   5   0   4   3  5  2
D22V6, multiclass
D22V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q GAIN MUTATED             1       3        0        0        0         1
  15Q GAIN WILD-TYPE           1       7        2        5        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q GAIN MUTATED           0         1          0          3          2
  15Q GAIN WILD-TYPE         2         4          2          4          7
                    vv
clus                 STAGE IV
  15Q GAIN MUTATED          0
  15Q GAIN WILD-TYPE        3
D22V8, multiclass

Clustering(23) Variable = 16p gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    0  3
  16P GAIN WILD-TYPE 17 16
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 16 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H 
       70.16        13.32         8.81 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       15.25         9.30        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       12.20        36.07         5.13         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              8.81               4.18 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             70.16              98.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             13.32              15.25 
[1] "8.8 - 70.2 (13.3)" "4.2 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    1             0
  16P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P GAIN MUTATED                                                                                          1
  16P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                     3
  16P GAIN WILD-TYPE                  45
D23V3, multiclass
                                                                                          clus
vv                                                                                         16P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    4
  16P GAIN WILD-TYPE   21   41
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  16P GAIN MUTATED    5  0   0   0   0
  16P GAIN WILD-TYPE 51  1   1   1   2
D23V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16P GAIN MUTATED    2  0   1   2   0   0   0  0  0
  16P GAIN WILD-TYPE 31  1   1   5   1   5   3  7  2
D23V6, multiclass
D23V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P GAIN MUTATED             0       2        0        0        0         0
  16P GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P GAIN MUTATED           0         2          1          0          0
  16P GAIN WILD-TYPE         2         3          1          7          9
                    vv
clus                 STAGE IV
  16P GAIN MUTATED          0
  16P GAIN WILD-TYPE        3
D23V8, multiclass

Clustering(24) Variable = 16q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    0  3
  16Q GAIN WILD-TYPE 17 16
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 16 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H 
       70.16        13.32         8.81 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       15.25         9.30        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       12.20        36.07         5.13         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              8.81               4.18 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             70.16              98.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.32              15.25 
[1] "8.8 - 70.2 (13.3)" "4.2 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D24V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    1             0
  16Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q GAIN MUTATED                                                                                          1
  16Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                     4
  16Q GAIN WILD-TYPE                  44
D24V3, multiclass
                                                                                          clus
vv                                                                                         16Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    5
  16Q GAIN WILD-TYPE   21   40
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  16Q GAIN MUTATED    6  0   0   0   0
  16Q GAIN WILD-TYPE 50  1   1   1   2
D24V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16Q GAIN MUTATED    2  0   1   3   0   0   0  0  0
  16Q GAIN WILD-TYPE 31  1   1   4   1   5   3  7  2
D24V6, multiclass
D24V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q GAIN MUTATED             0       2        0        0        0         0
  16Q GAIN WILD-TYPE           2       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q GAIN MUTATED           0         2          1          1          0
  16Q GAIN WILD-TYPE         2         3          1          6          9
                    vv
clus                 STAGE IV
  16Q GAIN MUTATED          0
  16Q GAIN WILD-TYPE        3
D24V8, multiclass

Clustering(25) Variable = 17p gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    4  1
  17P GAIN WILD-TYPE 13 18
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 31 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 18 
$`17P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2A6 
       13.32        36.69         5.13        12.03         8.94 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       13.68         9.99        44.52        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       12.20        36.07         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
        4.41        27.12         6.48         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5.13               4.18 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.69              98.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             12.03              17.56 
[1] "5.1 - 36.7 (12.0)" "4.2 - 98.8 (17.6)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D25V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    0             0
  17P GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P GAIN MUTATED                                                                                          2
  17P GAIN WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                     5
  17P GAIN WILD-TYPE                  43
D25V3, multiclass
                                                                                          clus
vv                                                                                         17P GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      43
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    5
  17P GAIN WILD-TYPE   20   40
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  17P GAIN MUTATED    6  0   0   0   0
  17P GAIN WILD-TYPE 50  1   1   1   2
D25V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17P GAIN MUTATED    4  0   0   1   0   1   0  0  0
  17P GAIN WILD-TYPE 29  1   2   6   1   4   3  7  2
D25V6, multiclass
D25V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P GAIN MUTATED             0       0        1        0        1         1
  17P GAIN WILD-TYPE           2      10        1        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P GAIN MUTATED           1         1          0          1          0
  17P GAIN WILD-TYPE         1         4          2          6          9
                    vv
clus                 STAGE IV
  17P GAIN MUTATED          0
  17P GAIN WILD-TYPE        3
D25V8, multiclass

Clustering(26) Variable = 17q gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    4  1
  17Q GAIN WILD-TYPE 13 18
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 31 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 18 
$`17Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29P TCGA-EE-A2A6 
       13.32        36.69         5.13        12.03         8.94 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
       13.68         9.99        44.52        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       12.20        36.07         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
        4.41        27.12         6.48         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5.13               4.18 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             36.69              98.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.03              17.56 
[1] "5.1 - 36.7 (12.0)" "4.2 - 98.8 (17.6)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D26V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    0             0
  17Q GAIN WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          1
  17Q GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                     5
  17Q GAIN WILD-TYPE                  43
D26V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    4
  17Q GAIN WILD-TYPE   20   41
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  17Q GAIN MUTATED    6  0   0   0   0
  17Q GAIN WILD-TYPE 50  1   1   1   2
D26V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17Q GAIN MUTATED    4  0   0   1   0   1   0  0  0
  17Q GAIN WILD-TYPE 29  1   2   6   1   4   3  7  2
D26V6, multiclass
D26V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        1        0        1         1
  17Q GAIN WILD-TYPE           2      10        1        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN MUTATED           1         1          0          1          0
  17Q GAIN WILD-TYPE         1         4          2          6          9
                    vv
clus                 STAGE IV
  17Q GAIN MUTATED          0
  17Q GAIN WILD-TYPE        3
D26V8, multiclass

Clustering(27) Variable = 18p gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    1  4
  18P GAIN WILD-TYPE 16 15
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                 31 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 15 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-EE-A29E 
       32.55        22.55        13.32        10.03        38.63 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       70.16        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
        9.30        35.80        51.12        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
       36.69        25.15        17.56        14.83        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        37.97         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             10.03               4.18 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             38.63              98.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             22.55              14.83 
[1] "10.0 - 38.6 (22.6)" "4.2 - 98.8 (14.8)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    1             0
  18P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          1
  18P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                     8
  18P GAIN WILD-TYPE                  40
D27V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      40
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    8
  18P GAIN WILD-TYPE   20   37
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                2                 20
  MALE                  8                 37
                    vv
clus                 M0 M1 M1A M1B M1C
  18P GAIN MUTATED    8  0   1   0   0
  18P GAIN WILD-TYPE 48  1   0   1   2
D27V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18P GAIN MUTATED    4  0   1   2   1   0   0  1  0
  18P GAIN WILD-TYPE 29  1   1   5   0   5   3  6  2
D27V6, multiclass
D27V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P GAIN MUTATED             2       2        0        0        0         0
  18P GAIN WILD-TYPE           0       8        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P GAIN MUTATED           0         1          1          2          1
  18P GAIN WILD-TYPE         2         4          1          5          8
                    vv
clus                 STAGE IV
  18P GAIN MUTATED          0
  18P GAIN WILD-TYPE        3
D27V8, multiclass

Clustering(28) Variable = 18q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    0  1
  18Q GAIN WILD-TYPE 17 18
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 35 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 18 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 
       32.55 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       37.97        38.63         4.41        27.12        12.03         6.48 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.94         4.18         8.81        24.85        84.72 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.55               4.18 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.55              98.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.55              14.83 
[1] "32.5 - 32.5 (32.5)" "4.2 - 98.8 (14.8)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 35 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J9         TCGA-D3-A2JD         TCGA-D3-A2JK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CE         TCGA-D3-A3MO 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29P         TCGA-EE-A29T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19J         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    1             0
  18Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          0
  18Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     3
  18Q GAIN WILD-TYPE                  45
D28V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      45
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    4
  18Q GAIN WILD-TYPE   22   41
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  18Q GAIN MUTATED    3  0   0   0   0
  18Q GAIN WILD-TYPE 53  1   1   1   2
D28V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18Q GAIN MUTATED    3  0   0   0   0   0   0  0  0
  18Q GAIN WILD-TYPE 30  1   2   7   1   5   3  7  2
D28V6, multiclass
D28V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q GAIN MUTATED             2       1        0        0        0         0
  18Q GAIN WILD-TYPE           0       9        2        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18Q GAIN MUTATED           0         0          0          0          0
  18Q GAIN WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  18Q GAIN MUTATED          0
  18Q GAIN WILD-TYPE        3
D28V8, multiclass

Clustering(29) Variable = 19p gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    0  2
  19P GAIN WILD-TYPE 17 17
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 17 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1I0 
       32.55        10.03 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       15.25        13.32         9.30        35.80        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             10.03               4.18 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             32.55              98.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             21.29              15.04 
[1] "10.0 - 32.5 (21.3)" "4.2 - 98.8 (15.0)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 34 
        TCGA-D3-A1Q6         TCGA-D3-A1Q7         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J9         TCGA-D3-A2JD         TCGA-D3-A2JK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CE         TCGA-D3-A3MO 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I2 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I4         TCGA-DA-A1I5         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A3F5         TCGA-DA-A3F8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A183         TCGA-EE-A20B         TCGA-EE-A20F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29H         TCGA-EE-A29M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29T         TCGA-EE-A2A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-FS-A1ZR         TCGA-GN-A262 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A265 
"19P GAIN WILD-TYPE" 
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    1             0
  19P GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P GAIN MUTATED                                                                                          1
  19P GAIN WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                     4
  19P GAIN WILD-TYPE                  44
D29V3, multiclass
                                                                                          clus
vv                                                                                         19P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    5
  19P GAIN WILD-TYPE   21   40
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  19P GAIN MUTATED    5  0   1   0   0
  19P GAIN WILD-TYPE 51  1   0   1   2
D29V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19P GAIN MUTATED    5  0   0   0   0   0   0  1  0
  19P GAIN WILD-TYPE 28  1   2   7   1   5   3  6  2
D29V6, multiclass
D29V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P GAIN MUTATED             2       1        0        1        0         1
  19P GAIN WILD-TYPE           0       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P GAIN MUTATED           0         0          0          0          1
  19P GAIN WILD-TYPE         2         5          2          7          8
                    vv
clus                 STAGE IV
  19P GAIN MUTATED          0
  19P GAIN WILD-TYPE        3
D29V8, multiclass

Clustering(30) Variable = 19q gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    1  2
  19Q GAIN WILD-TYPE 16 17
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 33 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 17 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CE TCGA-EE-A29T 
       32.55        13.32         6.48 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       15.25         9.30        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J 
       38.63         4.41        27.12        12.03         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              6.48               4.18 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.55              98.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             13.32              15.25 
[1] "6.5 - 32.5 (13.3)" "4.2 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    1             0
  19Q GAIN WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q GAIN MUTATED                                                                                          0
  19Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                     6
  19Q GAIN WILD-TYPE                  42
D30V3, multiclass
                                                                                          clus
vv                                                                                         19Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      42
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    4
  19Q GAIN WILD-TYPE   19   41
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  19Q GAIN MUTATED    7  0   0   0   0
  19Q GAIN WILD-TYPE 49  1   1   1   2
D30V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19Q GAIN MUTATED    5  0   0   1   0   0   0  0  1
  19Q GAIN WILD-TYPE 28  1   2   6   1   5   3  7  1
D30V6, multiclass
D30V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q GAIN MUTATED             2       1        0        1        0         1
  19Q GAIN WILD-TYPE           0       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q GAIN MUTATED           0         1          0          0          0
  19Q GAIN WILD-TYPE         2         4          2          7          9
                    vv
clus                 STAGE IV
  19Q GAIN MUTATED          0
  19Q GAIN WILD-TYPE        3
D30V8, multiclass

Clustering(31) Variable = 20p gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    4  8
  20P GAIN WILD-TYPE 13 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 24 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 11 
$`20P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       32.55        22.55        13.32        10.03        13.68        36.69 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A2A6 TCGA-ER-A19J 
       17.56        36.07         8.81         7.96         8.94         4.18 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       70.16        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
        9.30        35.80        51.12         9.99        44.52        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       14.83        12.20         5.13        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       27.12        12.03         6.48         8.81        24.85        84.72 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.18               4.41 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             36.69              98.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.500             18.195 
[1] "4.2 - 36.7 (13.5)" "4.4 - 98.8 (18.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                    3             0
  20P GAIN WILD-TYPE                  3             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                          4
  20P GAIN WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    17
  20P GAIN WILD-TYPE                  31
D31V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    17
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      31
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   20
  20P GAIN WILD-TYPE   18   25
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 20                 25
                    vv
clus                 M0 M1 M1A M1B M1C
  20P GAIN MUTATED   22  1   1   0   0
  20P GAIN WILD-TYPE 34  0   0   1   2
D31V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20P GAIN MUTATED   12  0   2   2   1   2   1  3  1
  20P GAIN WILD-TYPE 21  1   0   5   0   3   2  4  1
D31V6, multiclass
D31V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             2       5        1        0        3         1
  20P GAIN WILD-TYPE           0       5        1        5        5         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED           0         2          2          2          4
  20P GAIN WILD-TYPE         2         3          0          5          5
                    vv
clus                 STAGE IV
  20P GAIN MUTATED          1
  20P GAIN WILD-TYPE        2
D31V8, multiclass

Clustering(32) Variable = 20q gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    5  8
  20Q GAIN WILD-TYPE 12 11
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 23 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 11 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       32.55        22.55        13.32        10.03        13.68        36.69 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A2A6 
       17.56        36.07         8.81         7.96        38.63         8.94 
TCGA-ER-A19J 
        4.18 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       70.16        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
        9.30        35.80        51.12         9.99        44.52        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       14.83        12.20         5.13        37.97         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       12.03         6.48         8.81        24.85        84.72 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              4.18               4.41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             38.63              98.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.68              15.25 
[1] "4.2 - 38.6 (13.7)" "4.4 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                    3             0
  20Q GAIN WILD-TYPE                  3             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                          5
  20Q GAIN WILD-TYPE                                                                                        7
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                    20
  20Q GAIN WILD-TYPE                  28
D32V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    20
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        3
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  7
  REGIONAL LYMPH NODE                                                                                      28
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4   24
  20Q GAIN WILD-TYPE   18   21
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 24                 21
                    vv
clus                 M0 M1 M1A M1B M1C
  20Q GAIN MUTATED   23  1   1   1   0
  20Q GAIN WILD-TYPE 33  0   0   0   2
D32V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20Q GAIN MUTATED   12  0   2   3   1   2   1  4  1
  20Q GAIN WILD-TYPE 21  1   0   4   0   3   2  3  1
D32V6, multiclass
D32V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             2       5        1        0        3         1
  20Q GAIN WILD-TYPE           0       5        1        5        5         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED           0         2          2          3          4
  20Q GAIN WILD-TYPE         2         3          0          4          5
                    vv
clus                 STAGE IV
  20Q GAIN MUTATED          1
  20Q GAIN WILD-TYPE        2
D32V8, multiclass

Clustering(33) Variable = 21q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    0  2
  21Q GAIN WILD-TYPE 17 17
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 34 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 17 
$`21Q GAIN MUTATED`
TCGA-EE-A20H TCGA-EE-A29A 
        8.81         7.96 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
       17.56        14.83        12.20        36.07         5.13        37.97 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              7.96               4.18 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              8.81              98.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             8.385             16.405 
[1] "8.0 - 8.8 (8.4)"   "4.2 - 98.8 (16.4)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "21Q GAIN MUTATED"      
clus
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 2                 34 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29H         TCGA-EE-A29M 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29T         TCGA-EE-A2A6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-FS-A1ZR         TCGA-GN-A262 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A265 
"21Q GAIN WILD-TYPE" 
D33V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                    2             0
  21Q GAIN WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          0
  21Q GAIN WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                     2
  21Q GAIN WILD-TYPE                  46
D33V3, multiclass
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      46
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0    4
  21Q GAIN WILD-TYPE   22   41
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                0                 22
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  21Q GAIN MUTATED    4  0   0   0   0
  21Q GAIN WILD-TYPE 52  1   1   1   2
D33V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  21Q GAIN MUTATED    3  0   1   0   0   0   0  0  0
  21Q GAIN WILD-TYPE 30  1   1   7   1   5   3  7  2
D33V6, multiclass
D33V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q GAIN MUTATED             0       1        0        0        1         1
  21Q GAIN WILD-TYPE           2       9        2        5        7         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED           0         0          1          0          0
  21Q GAIN WILD-TYPE         2         5          1          7          9
                    vv
clus                 STAGE IV
  21Q GAIN MUTATED          0
  21Q GAIN WILD-TYPE        3
D33V8, multiclass

Clustering(34) Variable = 22q gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  5
  22Q GAIN WILD-TYPE 13 14
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                 27 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 14 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       22.55         9.30        10.03        36.69        25.15        17.56 
TCGA-EE-A20H TCGA-EE-A29M TCGA-GN-A265 
        8.81        27.12        84.72 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 
       15.25        13.32        35.80        51.12        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
       44.52        14.83        12.20        36.07         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       37.97        38.63         4.41        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
        4.18         8.81        24.85 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              8.81               4.18 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             84.72              98.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             22.55              13.68 
[1] "8.8 - 84.7 (22.6)" "4.2 - 98.8 (13.7)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                    2             1
  22Q GAIN WILD-TYPE                  4             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                          6
  22Q GAIN WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                     8
  22Q GAIN WILD-TYPE                  40
D34V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      40
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   14
  22Q GAIN WILD-TYPE   19   31
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                 14                 31
                    vv
clus                 M0 M1 M1A M1B M1C
  22Q GAIN MUTATED   13  0   1   1   0
  22Q GAIN WILD-TYPE 43  1   0   0   2
D34V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  22Q GAIN MUTATED    6  0   1   0   1   1   2  4  0
  22Q GAIN WILD-TYPE 27  1   1   7   0   4   1  3  2
D34V6, multiclass
D34V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q GAIN MUTATED             0       3        0        1        0         2
  22Q GAIN WILD-TYPE           2       7        2        4        8         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED           0         2          1          2          3
  22Q GAIN WILD-TYPE         2         3          1          5          6
                    vv
clus                 STAGE IV
  22Q GAIN MUTATED          0
  22Q GAIN WILD-TYPE        3
D34V8, multiclass

Clustering(35) Variable = 1p loss mutation analysis
D35V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    2  3
  1P LOSS WILD-TYPE 15 16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                31 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                3                16 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20H 
       22.55        13.68        36.69        17.56         8.81 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        9.99        44.52        25.15        14.83        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        5.13         7.96        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             8.81              4.18 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            36.69             98.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            17.56             14.83 
[1] "8.8 - 36.7 (17.6)" "4.2 - 98.8 (14.8)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D35V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    1             0
  1P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          1
  1P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     4
  1P LOSS WILD-TYPE                  44
D35V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     44
D35V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    5
  1P LOSS WILD-TYPE   21   40
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  1P LOSS MUTATED    6  0   0   0   0
  1P LOSS WILD-TYPE 50  1   1   1   2
D35V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1P LOSS MUTATED    2  0   0   0   1   2   0  1  0
  1P LOSS WILD-TYPE 31  1   2   7   0   3   3  6  2
D35V6, multiclass
D35V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P LOSS MUTATED             0       1        0        0        1         0
  1P LOSS WILD-TYPE           2       9        2        5        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1P LOSS MUTATED           0         0          0          2          2
  1P LOSS WILD-TYPE         2         5          2          5          7
                   vv
clus                STAGE IV
  1P LOSS MUTATED          0
  1P LOSS WILD-TYPE        3
D35V8, multiclass

Clustering(36) Variable = 1q loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    1  3
  1Q LOSS WILD-TYPE 16 16
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                32 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                16 
$`1Q LOSS MUTATED`
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A20H 
       13.68        36.69        25.15         8.81 

$`1Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       10.03         9.99        44.52        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.81              4.18 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            36.69             98.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           19.415            15.040 
[1] "8.8 - 36.7 (19.4)" "4.2 - 98.8 (15.0)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D36V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    1             0
  1Q LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q LOSS MUTATED                                                                                          2
  1Q LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                     1
  1Q LOSS WILD-TYPE                  47
D36V3, multiclass
                                                                                          clus
vv                                                                                         1Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     47
D36V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    3
  1Q LOSS WILD-TYPE   21   42
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  1Q LOSS MUTATED    4  0   0   0   0
  1Q LOSS WILD-TYPE 52  1   1   1   2
D36V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  1Q LOSS MUTATED    1  0   0   0   0   2   0  1  0
  1Q LOSS WILD-TYPE 32  1   2   7   1   3   3  6  2
D36V6, multiclass
D36V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q LOSS MUTATED             0       1        0        0        0         0
  1Q LOSS WILD-TYPE           2       9        2        5        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  1Q LOSS MUTATED           0         0          0          1          2
  1Q LOSS WILD-TYPE         2         5          2          6          7
                   vv
clus                STAGE IV
  1Q LOSS MUTATED          0
  1Q LOSS WILD-TYPE        3
D36V8, multiclass

Clustering(37) Variable = 2p loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    2  2
  2P LOSS WILD-TYPE 15 17
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                32 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                17 
$`2P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-DA-A1I2 TCGA-EE-A20B TCGA-EE-A20F 
       15.25        13.68        36.07         5.13 

$`2P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       12.20         8.81         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             5.13              4.18 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            36.07             98.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.465            16.195 
[1] "5.1 - 36.1 (14.5)" "4.2 - 98.8 (16.2)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D37V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                    1             0
  2P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P LOSS MUTATED                                                                                          1
  2P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                     5
  2P LOSS WILD-TYPE                  43
D37V3, multiclass
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D37V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4    3
  2P LOSS WILD-TYPE   18   42
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4                18
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  2P LOSS MUTATED    6  0   0   0   0
  2P LOSS WILD-TYPE 50  1   1   1   2
D37V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2P LOSS MUTATED    5  0   0   0   0   1   0  0  0
  2P LOSS WILD-TYPE 28  1   2   7   1   4   3  7  2
D37V6, multiclass
D37V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P LOSS MUTATED             0       0        0        1        3         1
  2P LOSS WILD-TYPE           2      10        2        4        5         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2P LOSS MUTATED           0         0          0          0          1
  2P LOSS WILD-TYPE         2         5          2          7          8
                   vv
clus                STAGE IV
  2P LOSS MUTATED          0
  2P LOSS WILD-TYPE        3
D37V8, multiclass

Clustering(38) Variable = 2q loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    2  1
  2Q LOSS WILD-TYPE 15 18
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                33 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                18 
$`2Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A20B TCGA-EE-A20F 
       15.25        36.07         5.13 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       14.83        12.20         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5.13              4.18 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            36.07             98.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            15.25             14.83 
[1] "5.1 - 36.1 (15.2)" "4.2 - 98.8 (14.8)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D38V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                    1             0
  2Q LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q LOSS MUTATED                                                                                          1
  2Q LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                     5
  2Q LOSS WILD-TYPE                  43
D38V3, multiclass
                                                                                          clus
vv                                                                                         2Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    2
  2Q LOSS WILD-TYPE   17   43
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5                17
  MALE                 2                43
                   vv
clus                M0 M1 M1A M1B M1C
  2Q LOSS MUTATED    5  0   0   1   0
  2Q LOSS WILD-TYPE 51  1   1   0   2
D38V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  2Q LOSS MUTATED    5  0   0   0   0   0   0  1  0
  2Q LOSS WILD-TYPE 28  1   2   7   1   5   3  6  2
D38V6, multiclass
D38V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q LOSS MUTATED             0       0        0        1        3         1
  2Q LOSS WILD-TYPE           2      10        2        4        5         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  2Q LOSS MUTATED           0         0          0          0          0
  2Q LOSS WILD-TYPE         2         5          2          7          9
                   vv
clus                STAGE IV
  2Q LOSS MUTATED          0
  2Q LOSS WILD-TYPE        3
D38V8, multiclass

Clustering(39) Variable = 3p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    2  4
  3P LOSS WILD-TYPE 15 15
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                15 
$`3P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-GN-A262 
       32.55        15.25        35.80        13.68        36.69        24.85 

$`3P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 
       13.32         9.30        51.12        10.03         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       25.15        17.56        14.83        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        8.81         7.96        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
       12.03         6.48         8.94         4.18         8.81        84.72 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.68              4.18 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            36.69             98.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            28.70             12.76 
[1] "13.7 - 36.7 (28.7)" "4.2 - 98.8 (12.8)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D39V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    0             0
  3P LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P LOSS MUTATED                                                                                          5
  3P LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                     4
  3P LOSS WILD-TYPE                  44
D39V3, multiclass
                                                                                          clus
vv                                                                                         3P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         3P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     44
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    5
  3P LOSS WILD-TYPE   18   40
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                18
  MALE                 5                40
                   vv
clus                M0 M1 M1A M1B M1C
  3P LOSS MUTATED    7  0   0   0   0
  3P LOSS WILD-TYPE 49  1   1   1   2
D39V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3P LOSS MUTATED    3  0   0   1   0   2   1  0  0
  3P LOSS WILD-TYPE 30  1   2   6   1   3   2  7  2
D39V6, multiclass
D39V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P LOSS MUTATED             1       1        0        1        0         0
  3P LOSS WILD-TYPE           1       9        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3P LOSS MUTATED           0         1          0          2          1
  3P LOSS WILD-TYPE         2         4          2          5          8
                   vv
clus                STAGE IV
  3P LOSS MUTATED          0
  3P LOSS WILD-TYPE        3
D39V8, multiclass

Clustering(40) Variable = 3q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    3  4
  3Q LOSS WILD-TYPE 14 15
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                7                29 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4                15 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A29H 
       32.55        15.25        35.80        13.68        36.69         4.41 
TCGA-GN-A262 
       24.85 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 
       13.32         9.30        51.12        10.03         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       25.15        17.56        14.83        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P 
        8.81         7.96        37.97        38.63        27.12        12.03 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        6.48         8.94         4.18         8.81        84.72 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.41              4.18 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            36.69             98.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            24.85             13.32 
[1] "4.4 - 36.7 (24.9)" "4.2 - 98.8 (13.3)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    0             0
  3Q LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q LOSS MUTATED                                                                                          4
  3Q LOSS WILD-TYPE                                                                                        8
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                     5
  3Q LOSS WILD-TYPE                  43
D40V3, multiclass
                                                                                          clus
vv                                                                                         3Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 8
  REGIONAL LYMPH NODE                                                                                     43
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    4
  3Q LOSS WILD-TYPE   17   41
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                17
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  3Q LOSS MUTATED    8  0   0   0   0
  3Q LOSS WILD-TYPE 48  1   1   1   2
D40V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  3Q LOSS MUTATED    4  0   0   1   0   2   1  0  0
  3Q LOSS WILD-TYPE 29  1   2   6   1   3   2  7  2
D40V6, multiclass
D40V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q LOSS MUTATED             1       1        1        1        0         0
  3Q LOSS WILD-TYPE           1       9        1        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  3Q LOSS MUTATED           0         1          0          2          1
  3Q LOSS WILD-TYPE         2         4          2          5          8
                   vv
clus                STAGE IV
  3Q LOSS MUTATED          0
  3Q LOSS WILD-TYPE        3
D40V8, multiclass

Clustering(41) Variable = 4p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    1  1
  4P LOSS WILD-TYPE 16 18
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                34 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                18 
$`4P LOSS MUTATED`
TCGA-DA-A1HW TCGA-EE-A29C 
       35.80        37.97 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25        13.32         9.30        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            35.80              4.18 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            37.97             98.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           36.885            14.255 
[1] "35.8 - 38.0 (36.9)" "4.2 - 98.8 (14.3)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                34 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-ER-A19J        TCGA-FS-A1ZR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D41V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                    0             0
  4P LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          1
  4P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     3
  4P LOSS WILD-TYPE                  45
D41V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1    3
  4P LOSS WILD-TYPE   21   42
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4P LOSS MUTATED    2  0   0   1   0
  4P LOSS WILD-TYPE 54  1   1   0   2
D41V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4P LOSS MUTATED    1  0   0   1   0   0   0  1  0
  4P LOSS WILD-TYPE 32  1   2   6   1   5   3  6  2
D41V6, multiclass
D41V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             0       0        0        1        0         0
  4P LOSS WILD-TYPE           2      10        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4P LOSS MUTATED           0         0          0          1          0
  4P LOSS WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  4P LOSS MUTATED          0
  4P LOSS WILD-TYPE        3
D41V8, multiclass
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                56 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE        TCGA-EE-A2GH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5        TCGA-EE-A2M6 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME        TCGA-EE-A2MG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP        TCGA-EE-A3AH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19O        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 

Clustering(42) Variable = 4q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    1  1
  4Q LOSS WILD-TYPE 16 18
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                34 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                18 
$`4Q LOSS MUTATED`
TCGA-DA-A1HW TCGA-EE-A29C 
       35.80        37.97 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25        13.32         9.30        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            35.80              4.18 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            37.97             98.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           36.885            14.255 
[1] "35.8 - 38.0 (36.9)" "4.2 - 98.8 (14.3)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                34 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29T        TCGA-EE-A2A6        TCGA-ER-A19J        TCGA-FS-A1ZR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A265 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D42V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                    0             0
  4Q LOSS WILD-TYPE                  6             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q LOSS MUTATED                                                                                          1
  4Q LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                     3
  4Q LOSS WILD-TYPE                  45
D42V3, multiclass
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     45
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE   21   42
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  4Q LOSS MUTATED    2  0   0   1   0
  4Q LOSS WILD-TYPE 54  1   1   0   2
D42V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  4Q LOSS MUTATED    1  0   0   1   0   0   0  1  0
  4Q LOSS WILD-TYPE 32  1   2   6   1   5   3  6  2
D42V6, multiclass
D42V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       0        0        1        0         0
  4Q LOSS WILD-TYPE           2      10        2        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  4Q LOSS MUTATED           0         0          0          1          0
  4Q LOSS WILD-TYPE         2         5          2          6          9
                   vv
clus                STAGE IV
  4Q LOSS MUTATED          0
  4Q LOSS WILD-TYPE        3
D42V8, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                56 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A183 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29M        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GE        TCGA-EE-A2GH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2M5        TCGA-EE-A2M6 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2ME        TCGA-EE-A2MG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2MH        TCGA-EE-A2MK        TCGA-EE-A2MP        TCGA-EE-A3AH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19O        TCGA-FS-A1YX        TCGA-FS-A1YY 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1Z7        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZF 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A1ZH        TCGA-FS-A1ZM        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 

Clustering(43) Variable = 5p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    4  0
  5P LOSS WILD-TYPE 13 19
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                32 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                19 
$`5P LOSS MUTATED`
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-GN-A262 
       37.97        38.63        27.12        24.85 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        7.96         4.41        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A265 
        8.81        84.72 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            24.85              4.18 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            38.63             98.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           32.545            13.500 
[1] "24.9 - 38.6 (32.5)" "4.2 - 98.8 (13.5)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D43V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                    0             1
  5P LOSS WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          2
  5P LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                     6
  5P LOSS WILD-TYPE                  42
D43V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     42
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    7
  5P LOSS WILD-TYPE   20   38
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                20
  MALE                 7                38
                   vv
clus                M0 M1 M1A M1B M1C
  5P LOSS MUTATED    6  0   0   0   0
  5P LOSS WILD-TYPE 50  1   1   1   2
D43V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5P LOSS MUTATED    4  0   0   1   0   0   1  0  0
  5P LOSS WILD-TYPE 29  1   2   6   1   5   2  7  2
D43V6, multiclass
D43V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       1        0        2        0         1
  5P LOSS WILD-TYPE           2       9        2        3        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5P LOSS MUTATED           0         1          0          1          0
  5P LOSS WILD-TYPE         2         4          2          6          9
                   vv
clus                STAGE IV
  5P LOSS MUTATED          0
  5P LOSS WILD-TYPE        3
D43V8, multiclass

Clustering(44) Variable = 5q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    6  5
  5Q LOSS WILD-TYPE 11 14
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               11                25 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                14 
$`5Q LOSS MUTATED`
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 
        6.35        15.25        35.80        10.03        44.52        36.69 
TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-GN-A262 
        8.81        37.97        38.63        27.12        24.85 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       13.32         9.30        51.12        13.68         9.99        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
       17.56        14.83        12.20        36.07         5.13         7.96 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        4.41        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A265 
       84.72 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             6.35              4.18 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            44.52             98.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            27.12             13.32 
[1] "6.3 - 44.5 (27.1)" "4.2 - 98.8 (13.3)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D44V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                    2             1
  5Q LOSS WILD-TYPE                  4             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          5
  5Q LOSS WILD-TYPE                                                                                        7
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    12
  5Q LOSS WILD-TYPE                  36
D44V3, multiclass
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       4
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 7
  REGIONAL LYMPH NODE                                                                                     36
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   13
  5Q LOSS WILD-TYPE   15   32
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               7                15
  MALE                13                32
                   vv
clus                M0 M1 M1A M1B M1C
  5Q LOSS MUTATED   15  0   1   0   1
  5Q LOSS WILD-TYPE 41  1   0   1   1
D44V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  5Q LOSS MUTATED   10  0   0   2   0   2   1  1  1
  5Q LOSS WILD-TYPE 23  1   2   5   1   3   2  6  1
D44V6, multiclass
D44V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             0       4        0        3        1         1
  5Q LOSS WILD-TYPE           2       6        2        2        7         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  5Q LOSS MUTATED           0         1          0          3          2
  5Q LOSS WILD-TYPE         2         4          2          4          7
                   vv
clus                STAGE IV
  5Q LOSS MUTATED          1
  5Q LOSS WILD-TYPE        2
D44V8, multiclass

Clustering(45) Variable = 6p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    1  3
  6P LOSS WILD-TYPE 16 16
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                32 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                16 
$`6P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-DA-A1I8 TCGA-EE-A29M 
       32.55        22.55        25.15        27.12 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       70.16        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       13.32         9.30        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
        9.99        44.52        36.69        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
        4.41        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            22.55              4.18 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            32.55             98.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           26.135            13.500 
[1] "22.6 - 32.5 (26.1)" "4.2 - 98.8 (13.5)" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                    0             1
  6P LOSS WILD-TYPE                  6             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P LOSS MUTATED                                                                                          2
  6P LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                     3
  6P LOSS WILD-TYPE                  45
D45V3, multiclass
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       6
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     45
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    3
  6P LOSS WILD-TYPE   19   42
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 3                42
                   vv
clus                M0 M1 M1A M1B M1C
  6P LOSS MUTATED    6  0   0   0   0
  6P LOSS WILD-TYPE 50  1   1   1   2
D45V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6P LOSS MUTATED    4  0   0   0   1   0   0  1  0
  6P LOSS WILD-TYPE 29  1   2   7   0   5   3  6  2
D45V6, multiclass
D45V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             1       1        0        1        1         0
  6P LOSS WILD-TYPE           1       9        2        4        7         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6P LOSS MUTATED           0         0          0          1          1
  6P LOSS WILD-TYPE         2         5          2          6          8
                   vv
clus                STAGE IV
  6P LOSS MUTATED          0
  6P LOSS WILD-TYPE        3
D45V8, multiclass

Clustering(46) Variable = 6q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    8 10
  6Q LOSS WILD-TYPE  9  9
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               18                18 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                 9 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I7 
       32.55        22.55        15.25        51.12         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       25.15        17.56        12.20        36.07         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       37.97         4.41        27.12         8.94         4.18         8.81 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CE 
       70.16        98.76        21.14        11.41         6.35        13.32 
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A3F8 
        9.30        35.80        10.03        13.68        44.52        14.83 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-GN-A262 TCGA-GN-A265 
        5.13        38.63        12.03         6.48        24.85        84.72 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             4.18              5.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            51.12             98.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           16.405            14.255 
[1] "4.2 - 51.1 (16.4)" "5.1 - 98.8 (14.3)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D46V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                    3             1
  6Q LOSS WILD-TYPE                  3             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                          8
  6Q LOSS WILD-TYPE                                                                                        4
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    19
  6Q LOSS WILD-TYPE                  29
D46V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               8
  REGIONAL LYMPH NODE                                                                                   19
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 4
  REGIONAL LYMPH NODE                                                                                     29
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      9   22
  6Q LOSS WILD-TYPE   13   23
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               9                13
  MALE                22                23
                   vv
clus                M0 M1 M1A M1B M1C
  6Q LOSS MUTATED   26  1   0   1   1
  6Q LOSS WILD-TYPE 30  0   1   0   1
D46V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  6Q LOSS MUTATED   15  0   2   1   1   2   2  5  1
  6Q LOSS WILD-TYPE 18  1   0   6   0   3   1  2  1
D46V6, multiclass
D46V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             1       4        2        3        4         0
  6Q LOSS WILD-TYPE           1       6        0        2        4         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  6Q LOSS MUTATED           1         1          2          4          3
  6Q LOSS WILD-TYPE         1         4          0          3          6
                   vv
clus                STAGE IV
  6Q LOSS MUTATED          2
  6Q LOSS WILD-TYPE        1
D46V8, multiclass

Clustering(47) Variable = 8p loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2  3
  8P LOSS WILD-TYPE 15 16
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                31 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                3                16 
$`8P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H 
       15.25         9.30        12.20        37.97         4.41 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        6.35        13.32        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        44.52        36.69        25.15        17.56        14.83 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29M 
       36.07         5.13         8.81         7.96        38.63        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 
       12.03         6.48         8.94         4.18         8.81        24.85 
TCGA-GN-A265 
       84.72 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.41              4.18 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.97             98.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.20             17.56 
[1] "4.4 - 38.0 (12.2)" "4.2 - 98.8 (17.6)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D47V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                    1             0
  8P LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P LOSS MUTATED                                                                                          1
  8P LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                     5
  8P LOSS WILD-TYPE                  43
D47V3, multiclass
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     43
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3    4
  8P LOSS WILD-TYPE   19   41
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 4                41
                   vv
clus                M0 M1 M1A M1B M1C
  8P LOSS MUTATED    6  0   0   1   0
  8P LOSS WILD-TYPE 50  1   1   0   2
D47V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  8P LOSS MUTATED    5  0   0   0   0   0   1  1  0
  8P LOSS WILD-TYPE 28  1   2   7   1   5   2  6  2
D47V6, multiclass
D47V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             0       1        1        2        0         1
  8P LOSS WILD-TYPE           2       9        1        3        8         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  8P LOSS MUTATED           0         1          0          0          0
  8P LOSS WILD-TYPE         2         4          2          7          9
                   vv
clus                STAGE IV
  8P LOSS MUTATED          0
  8P LOSS WILD-TYPE        3
D47V8, multiclass

Clustering(48) Variable = 9p loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    7 11
  9P LOSS WILD-TYPE 10  8
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                18 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                 8 
$`9P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW 
       32.55        70.16         6.35        15.25         9.30        35.80 
TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-EE-A20B 
       51.12        13.68         9.99        44.52        25.15        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29P TCGA-FS-A1ZR 
        5.13         8.81        37.97        38.63        12.03         8.81 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-DA-A1I0 
       98.76        22.55        21.14        11.41        13.32        10.03 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29H 
       36.69        17.56        14.83        12.20         7.96         4.41 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-GN-A262 TCGA-GN-A265 
       27.12         6.48         8.94         4.18        24.85        84.72 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             5.13              4.18 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            70.16             98.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           20.200            14.075 
[1] "5.1 - 70.2 (20.2)" "4.2 - 98.8 (14.1)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                    5             0
  9P LOSS WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                          9
  9P LOSS WILD-TYPE                                                                                        3
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                    24
  9P LOSS WILD-TYPE                  24
D48V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   24
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 3
  REGIONAL LYMPH NODE                                                                                     24
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13   25
  9P LOSS WILD-TYPE    9   20
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              13                 9
  MALE                25                20
                   vv
clus                M0 M1 M1A M1B M1C
  9P LOSS MUTATED   31  0   0   1   2
  9P LOSS WILD-TYPE 25  1   1   0   0
D48V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  9P LOSS MUTATED   19  0   1   5   0   3   3  3  0
  9P LOSS WILD-TYPE 14  1   1   2   1   2   0  4  2
D48V6, multiclass
D48V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             2       3        0        3        7         1
  9P LOSS WILD-TYPE           0       7        2        2        1         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9P LOSS MUTATED           2         3          1          4          5
  9P LOSS WILD-TYPE         0         2          1          3          4
                   vv
clus                STAGE IV
  9P LOSS MUTATED          2
  9P LOSS WILD-TYPE        1
D48V8, multiclass

Clustering(49) Variable = 9q loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    5  8
  9Q LOSS WILD-TYPE 12 11
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13                23 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                8                11 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       32.55        15.25        35.80        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29P TCGA-FS-A1ZR 
       25.15        36.07         5.13         8.81        12.03         8.81 
TCGA-GN-A262 
       24.85 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A3F5 
       13.32         9.30        51.12        10.03        36.69        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       14.83        12.20         7.96        37.97        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-GN-A265 
       27.12         6.48         8.94         4.18        84.72 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             5.13              4.18 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            44.52             98.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            15.25             14.83 
[1] "5.1 - 44.5 (15.2)" "4.2 - 98.8 (14.8)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D49V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                    5             0
  9Q LOSS WILD-TYPE                  1             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                          7
  9Q LOSS WILD-TYPE                                                                                        5
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    17
  9Q LOSS WILD-TYPE                  31
D49V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   17
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       1
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 5
  REGIONAL LYMPH NODE                                                                                     31
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13   16
  9Q LOSS WILD-TYPE    9   29
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              13                 9
  MALE                16                29
                   vv
clus                M0 M1 M1A M1B M1C
  9Q LOSS MUTATED   21  0   0   1   2
  9Q LOSS WILD-TYPE 35  1   1   0   0
D49V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  9Q LOSS MUTATED   16  0   1   1   0   2   2  2  0
  9Q LOSS WILD-TYPE 17  1   1   6   1   3   1  5  2
D49V6, multiclass
D49V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             2       2        0        2        6         1
  9Q LOSS WILD-TYPE           0       8        2        3        2         2
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  9Q LOSS MUTATED           2         1          1          2          2
  9Q LOSS WILD-TYPE         0         4          1          5          7
                   vv
clus                STAGE IV
  9Q LOSS MUTATED          2
  9Q LOSS WILD-TYPE        1
D49V8, multiclass

Clustering(50) Variable = 10p loss mutation analysis
D50V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    8 11
  10P LOSS WILD-TYPE  9  8
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                19                 17 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                  8 
$`10P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO 
       32.55        70.16        98.76         6.35        13.32         9.30 
TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       35.80        13.68         9.99        44.52        36.69        25.15 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
       36.07         5.13         8.81         4.41        27.12        12.03 
TCGA-FS-A1ZR 
        8.81 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-DA-A1HY TCGA-DA-A1I0 
       22.55        21.14        11.41        15.25        51.12        10.03 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       17.56        14.83        12.20         7.96        37.97        38.63 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94         4.18        24.85        84.72 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              4.41               4.18 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.76              84.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             13.68              15.25 
[1] "4.4 - 98.8 (13.7)" "4.2 - 84.7 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D50V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                    4             1
  10P LOSS WILD-TYPE                  2             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                          9
  10P LOSS WILD-TYPE                                                                                        3
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    22
  10P LOSS WILD-TYPE                  26
D50V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    22
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  3
  REGIONAL LYMPH NODE                                                                                      26
D50V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     15   21
  10P LOSS WILD-TYPE    7   24
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               15                  7
  MALE                 21                 24
                    vv
clus                 M0 M1 M1A M1B M1C
  10P LOSS MUTATED   33  0   0   0   2
  10P LOSS WILD-TYPE 23  1   1   1   0
D50V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  10P LOSS MUTATED   22  0   1   4   0   4   3  1  0
  10P LOSS WILD-TYPE 11  1   1   3   1   1   0  6  2
D50V6, multiclass
D50V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             2       5        1        3        7         1
  10P LOSS WILD-TYPE           0       5        1        2        1         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS MUTATED           2         4          1          3          4
  10P LOSS WILD-TYPE         0         1          1          4          5
                    vv
clus                 STAGE IV
  10P LOSS MUTATED          2
  10P LOSS WILD-TYPE        1
D50V8, multiclass

Clustering(51) Variable = 10q loss mutation analysis
D51V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   11 13
  10Q LOSS WILD-TYPE  6  6
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                24                 12 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                13                  6 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2JK TCGA-D3-A3C6 
       32.55        70.16        98.76        22.55         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       13.32         9.30        35.80        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       36.69        25.15        14.83        36.07         5.13         8.81 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A2A6 TCGA-FS-A1ZR TCGA-GN-A262 
        4.41        27.12        12.03         8.94         8.81        24.85 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A3F5 TCGA-EE-A183 
       21.14        11.41        51.12        10.03        17.56        12.20 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29T TCGA-ER-A19J TCGA-GN-A265 
        7.96        37.97        38.63         6.48         4.18        84.72 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              4.41               4.18 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.76              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             15.04              14.88 
[1] "4.4 - 98.8 (15.0)" "4.2 - 84.7 (14.9)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D51V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                    5             1
  10Q LOSS WILD-TYPE                  1             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                         11
  10Q LOSS WILD-TYPE                                                                                        1
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                    28
  10Q LOSS WILD-TYPE                  20
D51V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               11
  REGIONAL LYMPH NODE                                                                                    28
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        1
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  1
  REGIONAL LYMPH NODE                                                                                      20
D51V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19   26
  10Q LOSS WILD-TYPE    3   19
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               19                  3
  MALE                 26                 19
                    vv
clus                 M0 M1 M1A M1B M1C
  10Q LOSS MUTATED   38  0   0   1   2
  10Q LOSS WILD-TYPE 18  1   1   0   0
D51V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  10Q LOSS MUTATED   25  0   1   4   1   5   3  2  0
  10Q LOSS WILD-TYPE  8  1   1   3   0   0   0  5  2
D51V6, multiclass
D51V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             2       5        2        4        7         2
  10Q LOSS WILD-TYPE           0       5        0        1        1         1
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED           2         4          1          5          4
  10Q LOSS WILD-TYPE         0         1          1          2          5
                    vv
clus                 STAGE IV
  10Q LOSS MUTATED          2
  10Q LOSS WILD-TYPE        1
D51V8, multiclass

Clustering(52) Variable = 11p loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    4  5
  11P LOSS WILD-TYPE 13 14
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 9                 27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 14 
$`11P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I5 TCGA-DA-A1I8 
       32.55        22.55         9.30        35.80        44.52        25.15 
TCGA-EE-A29C TCGA-EE-A29M TCGA-GN-A262 
       37.97        27.12        24.85 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       70.16        98.76        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       13.32        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
        7.96        38.63         4.41        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        84.72 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              9.30               4.18 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             44.52              98.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             27.12              12.20 
[1] "9.3 - 44.5 (27.1)" "4.2 - 98.8 (12.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D52V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                    1             1
  11P LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                          3
  11P LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                     8
  11P LOSS WILD-TYPE                  40
D52V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      40
D52V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7    6
  11P LOSS WILD-TYPE   15   39
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                7                 15
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  11P LOSS MUTATED    8  0   0   0   2
  11P LOSS WILD-TYPE 48  1   1   1   0
D52V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11P LOSS MUTATED    4  0   0   1   1   0   2  1  1
  11P LOSS WILD-TYPE 29  1   2   6   0   5   1  6  1
D52V6, multiclass
D52V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       0        0        2        0         0
  11P LOSS WILD-TYPE           1      10        2        3        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS MUTATED           0         1          0          2          1
  11P LOSS WILD-TYPE         2         4          2          5          8
                    vv
clus                 STAGE IV
  11P LOSS MUTATED          2
  11P LOSS WILD-TYPE        1
D52V8, multiclass

Clustering(53) Variable = 11q loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    4  5
  11Q LOSS WILD-TYPE 13 14
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 14 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I5 
       32.55        98.76        22.55         9.30        35.80        44.52 
TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29M 
       25.15        37.97        27.12 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       70.16        21.14        11.41         6.35        15.25        13.32 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A3F5 
       51.12        10.03        13.68         9.99        36.69        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
       38.63         4.41        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              9.30               4.18 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             98.76              84.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             32.55              12.20 
[1] "9.3 - 98.8 (32.5)" "4.2 - 84.7 (12.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D53V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                    2             1
  11Q LOSS WILD-TYPE                  4             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          2
  11Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    10
  11Q LOSS WILD-TYPE                  38
D53V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      38
D53V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      8    7
  11Q LOSS WILD-TYPE   14   38
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                8                 14
  MALE                  7                 38
                    vv
clus                 M0 M1 M1A M1B M1C
  11Q LOSS MUTATED   11  0   0   0   2
  11Q LOSS WILD-TYPE 45  1   1   1   0
D53V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  11Q LOSS MUTATED    6  0   0   2   1   0   2  1  1
  11Q LOSS WILD-TYPE 27  1   2   5   0   5   1  6  1
D53V6, multiclass
D53V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       0        0        3        0         0
  11Q LOSS WILD-TYPE           1      10        2        2        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED           1         1          0          2          2
  11Q LOSS WILD-TYPE         1         4          2          5          7
                    vv
clus                 STAGE IV
  11Q LOSS MUTATED          2
  11Q LOSS WILD-TYPE        1
D53V8, multiclass

Clustering(54) Variable = 12p loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  12P LOSS WILD-TYPE 17 19
12P LOSS WILD-TYPE 
                36 
[1] 19
$`12P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
        7.96        37.97        38.63         4.41        27.12        12.03 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94         4.18         8.81        24.85        84.72 

12P LOSS WILD-TYPE 
              4.18 
12P LOSS WILD-TYPE 
             98.76 
12P LOSS WILD-TYPE 
             15.04 
[1] "4.2 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D54V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                    0             0
  12P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P LOSS MUTATED                                                                                          1
  12P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                     2
  12P LOSS WILD-TYPE                  46
D54V3, multiclass
                                                                                          clus
vv                                                                                         12P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      46
D54V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE   19   45
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  0                 45
                    vv
clus                 M0 M1 M1A M1B M1C
  12P LOSS MUTATED    2  0   0   0   1
  12P LOSS WILD-TYPE 54  1   1   1   1
D54V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12P LOSS MUTATED    2  0   0   0   0   0   1  0  0
  12P LOSS WILD-TYPE 31  1   2   7   1   5   2  7  2
D54V6, multiclass
D54V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P LOSS MUTATED             0       1        0        0        1         0
  12P LOSS WILD-TYPE           2       9        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12P LOSS MUTATED           0         0          0          0          0
  12P LOSS WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  12P LOSS MUTATED          1
  12P LOSS WILD-TYPE        2
D54V8, multiclass

Clustering(55) Variable = 12q loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  12Q LOSS WILD-TYPE 17 19
12Q LOSS WILD-TYPE 
                36 
[1] 19
$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P 
        7.96        37.97        38.63         4.41        27.12        12.03 
TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        6.48         8.94         4.18         8.81        24.85        84.72 

12Q LOSS WILD-TYPE 
              4.18 
12Q LOSS WILD-TYPE 
             98.76 
12Q LOSS WILD-TYPE 
             15.04 
[1] "4.2 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D55V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                    0             0
  12Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          1
  12Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     3
  12Q LOSS WILD-TYPE                  45
D55V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    1
  12Q LOSS WILD-TYPE   19   44
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  1                 44
                    vv
clus                 M0 M1 M1A M1B M1C
  12Q LOSS MUTATED    2  0   0   0   1
  12Q LOSS WILD-TYPE 54  1   1   1   1
D55V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  12Q LOSS MUTATED    2  0   0   0   0   0   1  0  0
  12Q LOSS WILD-TYPE 31  1   2   7   1   5   2  7  2
D55V6, multiclass
D55V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             0       1        0        0        1         0
  12Q LOSS WILD-TYPE           2       9        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  12Q LOSS MUTATED           0         0          0          0          0
  12Q LOSS WILD-TYPE         2         5          2          7          9
                    vv
clus                 STAGE IV
  12Q LOSS MUTATED          1
  12Q LOSS WILD-TYPE        2
D55V8, multiclass

Clustering(56) Variable = 13q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    3  3
  13Q LOSS WILD-TYPE 14 16
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 16 
$`13Q LOSS MUTATED`
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T 
       13.68         9.99        25.15        37.97        27.12         6.48 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       10.03        44.52        36.69        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13         8.81         7.96        38.63         4.41 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
       12.03         8.94         4.18         8.81        24.85        84.72 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              6.48               4.18 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             37.97              98.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            19.415             15.040 
[1] "6.5 - 38.0 (19.4)" "4.2 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D56V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                    0             1
  13Q LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          2
  13Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                     7
  13Q LOSS WILD-TYPE                  41
D56V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      41
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    6
  13Q LOSS WILD-TYPE   18   39
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  13Q LOSS MUTATED    7  0   0   1   1
  13Q LOSS WILD-TYPE 49  1   1   0   1
D56V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  13Q LOSS MUTATED    3  0   0   0   0   2   1  2  1
  13Q LOSS WILD-TYPE 30  1   2   7   1   3   2  5  1
D56V6, multiclass
D56V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        0        2        1         0
  13Q LOSS WILD-TYPE           2      10        2        3        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED           0         0          0          1          2
  13Q LOSS WILD-TYPE         2         5          2          6          7
                    vv
clus                 STAGE IV
  13Q LOSS MUTATED          1
  13Q LOSS WILD-TYPE        2
D56V8, multiclass

Clustering(57) Variable = 14q loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    5  2
  14Q LOSS WILD-TYPE 12 17
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 29 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 2                 17 
$`14Q LOSS MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HY TCGA-DA-A1I5 TCGA-DA-A3F5 TCGA-EE-A29C TCGA-EE-A2A6 
       13.32        51.12        44.52        17.56        37.97         8.94 
TCGA-FS-A1ZR 
        8.81 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        6.35        15.25         9.30        35.80        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B 
        9.99        36.69        25.15        14.83        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        5.13         8.81         7.96        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-GN-A262 TCGA-GN-A265 
       12.03         6.48         4.18        24.85        84.72 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              8.81               4.18 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             51.12              98.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             17.56              14.83 
[1] "8.8 - 51.1 (17.6)" "4.2 - 98.8 (14.8)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D57V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                    2             0
  14Q LOSS WILD-TYPE                  4             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                          3
  14Q LOSS WILD-TYPE                                                                                        9
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    13
  14Q LOSS WILD-TYPE                  35
D57V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    13
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        4
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  9
  REGIONAL LYMPH NODE                                                                                      35
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5   13
  14Q LOSS WILD-TYPE   17   32
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                5                 17
  MALE                 13                 32
                    vv
clus                 M0 M1 M1A M1B M1C
  14Q LOSS MUTATED   16  0   0   0   2
  14Q LOSS WILD-TYPE 40  1   1   1   0
D57V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  14Q LOSS MUTATED   12  0   0   2   0   0   2  2  0
  14Q LOSS WILD-TYPE 21  1   2   5   1   5   1  5  2
D57V6, multiclass
D57V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             1       3        1        1        5         0
  14Q LOSS WILD-TYPE           1       7        1        4        3         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED           0         2          0          0          3
  14Q LOSS WILD-TYPE         2         3          2          7          6
                    vv
clus                 STAGE IV
  14Q LOSS MUTATED          2
  14Q LOSS WILD-TYPE        1
D57V8, multiclass

Clustering(58) Variable = 15q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    1  1
  15Q LOSS WILD-TYPE 16 18
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 34 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 18 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29P 
       15.25        12.03 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
       37.97        38.63         4.41        27.12         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             12.03               4.18 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             15.25              98.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            13.640             16.195 
[1] "12.0 - 15.2 (13.6)" "4.2 - 98.8 (16.2)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 34 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3CE         TCGA-D3-A3MO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29C         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29M         TCGA-EE-A29T         TCGA-EE-A2A6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-FS-A1ZR         TCGA-GN-A262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A265 
"15Q LOSS WILD-TYPE" 
D58V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    0             0
  15Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q LOSS MUTATED                                                                                          2
  15Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                     4
  15Q LOSS WILD-TYPE                  44
D58V3, multiclass
                                                                                          clus
vv                                                                                         15Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      44
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    2
  15Q LOSS WILD-TYPE   18   43
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  15Q LOSS MUTATED    5  0   0   1   0
  15Q LOSS WILD-TYPE 51  1   1   0   2
D58V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  15Q LOSS MUTATED    4  0   0   0   0   0   1  1  0
  15Q LOSS WILD-TYPE 29  1   2   7   1   5   2  6  2
D58V6, multiclass
D58V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       1        0        1        1         0
  15Q LOSS WILD-TYPE           2       9        2        4        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS MUTATED           1         1          0          0          0
  15Q LOSS WILD-TYPE         1         4          2          7          9
                    vv
clus                 STAGE IV
  15Q LOSS MUTATED          0
  15Q LOSS WILD-TYPE        3
D58V8, multiclass

Clustering(59) Variable = 16p loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 16 16
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 32 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 16 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-GN-A262 
       32.55        35.80        13.68        24.85 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 
       15.25        13.32         9.30        51.12        10.03         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       44.52        36.69        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J 
        4.41        27.12        12.03         6.48         8.94         4.18 
TCGA-FS-A1ZR TCGA-GN-A265 
        8.81        84.72 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.68               4.18 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.80              98.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            28.700             14.075 
[1] "13.7 - 35.8 (28.7)" "4.2 - 98.8 (14.1)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                    0             0
  16P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P LOSS MUTATED                                                                                          1
  16P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                     4
  16P LOSS WILD-TYPE                  44
D59V3, multiclass
                                                                                          clus
vv                                                                                         16P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         16P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      44
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    2
  16P LOSS WILD-TYPE   19   43
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  16P LOSS MUTATED    4  0   0   0   0
  16P LOSS WILD-TYPE 52  1   1   1   2
D59V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16P LOSS MUTATED    2  0   0   1   0   1   0  0  0
  16P LOSS WILD-TYPE 31  1   2   6   1   4   3  7  2
D59V6, multiclass
D59V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P LOSS MUTATED             1       0        0        0        1         0
  16P LOSS WILD-TYPE           1      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS MUTATED           0         0          0          1          1
  16P LOSS WILD-TYPE         2         5          2          6          8
                    vv
clus                 STAGE IV
  16P LOSS MUTATED          0
  16P LOSS WILD-TYPE        3
D59V8, multiclass

Clustering(60) Variable = 16q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    2  4
  16Q LOSS WILD-TYPE 15 15
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 6                 30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 15 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-GN-A262 
       32.55        35.80        13.68         9.99        14.83        24.85 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I5 
       15.25        13.32         9.30        51.12        10.03        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       36.69        25.15        17.56        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        8.81         7.96        37.97        38.63         4.41        27.12 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
       12.03         6.48         8.94         4.18         8.81        84.72 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              9.99               4.18 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.80              98.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            19.840             14.285 
[1] "10.0 - 35.8 (19.8)" "4.2 - 98.8 (14.3)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D60V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                    1             0
  16Q LOSS WILD-TYPE                  5             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          2
  16Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                     7
  16Q LOSS WILD-TYPE                  41
D60V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      41
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5    5
  16Q LOSS WILD-TYPE   17   40
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                5                 17
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  16Q LOSS MUTATED    7  0   0   1   0
  16Q LOSS WILD-TYPE 49  1   1   0   2
D60V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  16Q LOSS MUTATED    3  0   0   1   0   3   0  1  0
  16Q LOSS WILD-TYPE 30  1   2   6   1   2   3  6  2
D60V6, multiclass
D60V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             1       0        0        0        1         0
  16Q LOSS WILD-TYPE           1      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED           1         0          0          3          1
  16Q LOSS WILD-TYPE         1         5          2          4          8
                    vv
clus                 STAGE IV
  16Q LOSS MUTATED          0
  16Q LOSS WILD-TYPE        3
D60V8, multiclass

Clustering(61) Variable = 17p loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    5  2
  17P LOSS WILD-TYPE 12 17
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 17 
$`17P LOSS MUTATED`
TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        9.30        35.80        51.12        37.97         4.41        27.12 
TCGA-EE-A29T 
        6.48 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        6.35        15.25        13.32        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
       44.52        36.69        25.15        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29P 
       36.07         5.13         8.81         7.96        38.63        12.03 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.94         4.18         8.81        24.85        84.72 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              4.41               4.18 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.12              98.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             27.12              14.83 
[1] "4.4 - 51.1 (27.1)" "4.2 - 98.8 (14.8)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D61V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                    0             1
  17P LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          2
  17P LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                     9
  17P LOSS WILD-TYPE                  39
D61V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      39
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    6
  17P LOSS WILD-TYPE   16   39
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                 16
  MALE                  6                 39
                    vv
clus                 M0 M1 M1A M1B M1C
  17P LOSS MUTATED   10  0   0   1   1
  17P LOSS WILD-TYPE 46  1   1   0   1
D61V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17P LOSS MUTATED    6  0   0   1   0   0   2  2  1
  17P LOSS WILD-TYPE 27  1   2   6   1   5   1  5  1
D61V6, multiclass
D61V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             0       2        1        2        0         1
  17P LOSS WILD-TYPE           2       8        1        3        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS MUTATED           0         1          0          1          1
  17P LOSS WILD-TYPE         2         4          2          6          8
                    vv
clus                 STAGE IV
  17P LOSS MUTATED          1
  17P LOSS WILD-TYPE        2
D61V8, multiclass

Clustering(62) Variable = 17q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    1  1
  17Q LOSS WILD-TYPE 16 18
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 34 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 18 
$`17Q LOSS MUTATED`
TCGA-DA-A1HW TCGA-EE-A29C 
       35.80        37.97 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        15.25        13.32         9.30        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       38.63         4.41        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.18         8.81        24.85        84.72 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             35.80               4.18 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             37.97              98.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            36.885             14.255 
[1] "35.8 - 38.0 (36.9)" "4.2 - 98.8 (14.3)" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 34 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I7         TCGA-DA-A1I8         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A183         TCGA-EE-A20B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20F         TCGA-EE-A20H         TCGA-EE-A29A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29E         TCGA-EE-A29H         TCGA-EE-A29M 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29T         TCGA-EE-A2A6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-FS-A1ZR         TCGA-GN-A262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A265 
"17Q LOSS WILD-TYPE" 
D62V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    0             0
  17Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          0
  17Q LOSS WILD-TYPE                                                                                       12
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                     5
  17Q LOSS WILD-TYPE                  43
D62V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 12
  REGIONAL LYMPH NODE                                                                                      43
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    3
  17Q LOSS WILD-TYPE   20   42
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 20
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  17Q LOSS MUTATED    4  0   0   0   1
  17Q LOSS WILD-TYPE 52  1   1   1   1
D62V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  17Q LOSS MUTATED    3  0   0   1   0   0   1  0  0
  17Q LOSS WILD-TYPE 30  1   2   6   1   5   2  7  2
D62V6, multiclass
D62V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             0       1        0        1        0         1
  17Q LOSS WILD-TYPE           2       9        2        4        8         2
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS MUTATED           0         0          0          1          0
  17Q LOSS WILD-TYPE         2         5          2          6          9
                    vv
clus                 STAGE IV
  17Q LOSS MUTATED          1
  17Q LOSS WILD-TYPE        2
D62V8, multiclass

Clustering(63) Variable = 18p loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    5  5
  18P LOSS WILD-TYPE 12 14
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                 26 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                 14 
$`18P LOSS MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B 
       70.16        15.25        13.68        36.69        17.56        36.07 
TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29T TCGA-FS-A1ZR 
        7.96        27.12         6.48         8.81 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 
       13.32         9.30        35.80        51.12        10.03         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H 
       44.52        25.15        14.83        12.20         5.13         8.81 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A19J 
       37.97        38.63         4.41        12.03         8.94         4.18 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.48               4.18 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             70.16              98.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            16.405             14.075 
[1] "6.5 - 70.2 (16.4)" "4.2 - 98.8 (14.1)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                    1             1
  18P LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          6
  18P LOSS WILD-TYPE                                                                                        6
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                     8
  18P LOSS WILD-TYPE                  40
D63V3, multiclass
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  6
  REGIONAL LYMPH NODE                                                                                      40
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      6   10
  18P LOSS WILD-TYPE   16   35
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                6                 16
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  18P LOSS MUTATED   15  0   0   0   0
  18P LOSS WILD-TYPE 41  1   1   1   2
D63V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18P LOSS MUTATED    7  0   1   1   0   2   1  1  2
  18P LOSS WILD-TYPE 26  1   1   6   1   3   2  6  0
D63V6, multiclass
D63V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             0       0        0        2        5         0
  18P LOSS WILD-TYPE           2      10        2        3        3         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18P LOSS MUTATED           0         2          1          1          2
  18P LOSS WILD-TYPE         2         3          1          6          7
                    vv
clus                 STAGE IV
  18P LOSS MUTATED          0
  18P LOSS WILD-TYPE        3
D63V8, multiclass

Clustering(64) Variable = 18q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    6  6
  18Q LOSS WILD-TYPE 11 13
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                12                 24 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                 13 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1I2 TCGA-DA-A1I7 
       70.16        22.55        15.25        13.32        13.68        36.69 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T 
       17.56        36.07         7.96        27.12        12.03         6.48 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3MO 
       32.55        98.76        21.14        11.41         6.35         9.30 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       35.80        51.12        10.03         9.99        44.52        25.15 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E 
       14.83        12.20         5.13         8.81        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        4.41         8.94         4.18         8.81        24.85        84.72 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              6.48               4.18 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             70.16              98.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            16.405             13.515 
[1] "6.5 - 70.2 (16.4)" "4.2 - 98.8 (13.5)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                    1             1
  18Q LOSS WILD-TYPE                  5             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          4
  18Q LOSS WILD-TYPE                                                                                        8
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    11
  18Q LOSS WILD-TYPE                  37
D64V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        5
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  8
  REGIONAL LYMPH NODE                                                                                      37
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7   10
  18Q LOSS WILD-TYPE   15   35
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                7                 15
  MALE                 10                 35
                    vv
clus                 M0 M1 M1A M1B M1C
  18Q LOSS MUTATED   16  0   0   1   0
  18Q LOSS WILD-TYPE 40  1   1   0   2
D64V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  18Q LOSS MUTATED    7  0   1   2   1   2   1  2  1
  18Q LOSS WILD-TYPE 26  1   1   5   0   3   2  5  1
D64V6, multiclass
D64V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             0       0        0        2        4         0
  18Q LOSS WILD-TYPE           2      10        2        3        4         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED           1         3          1          2          2
  18Q LOSS WILD-TYPE         1         2          1          5          7
                    vv
clus                 STAGE IV
  18Q LOSS MUTATED          0
  18Q LOSS WILD-TYPE        3
D64V8, multiclass

Clustering(65) Variable = 19p loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    1  3
  19P LOSS WILD-TYPE 16 16
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 32 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 16 
$`19P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1HW TCGA-DA-A1I8 TCGA-EE-A29H 
       22.55        35.80        25.15         4.41 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
       15.25        13.32         9.30        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 
        9.99        44.52        36.69        17.56        14.83        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        37.97        38.63 
TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       27.12        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              4.41               4.18 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             35.80              98.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            23.850             14.255 
[1] "4.4 - 35.8 (23.9)" "4.2 - 98.8 (14.3)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                    0             0
  19P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P LOSS MUTATED                                                                                          1
  19P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                     5
  19P LOSS WILD-TYPE                  43
D65V3, multiclass
                                                                                          clus
vv                                                                                         19P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      43
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      4    2
  19P LOSS WILD-TYPE   18   43
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  19P LOSS MUTATED    4  0   0   1   1
  19P LOSS WILD-TYPE 52  1   1   0   1
D65V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19P LOSS MUTATED    1  0   0   1   1   0   1  2  0
  19P LOSS WILD-TYPE 32  1   2   6   0   5   2  5  2
D65V6, multiclass
D65V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             0       0        1        0        0         0
  19P LOSS WILD-TYPE           2      10        1        5        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS MUTATED           0         0          0          2          1
  19P LOSS WILD-TYPE         2         5          2          5          8
                    vv
clus                 STAGE IV
  19P LOSS MUTATED          1
  19P LOSS WILD-TYPE        2
D65V8, multiclass

Clustering(66) Variable = 19q loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    2  2
  19Q LOSS WILD-TYPE 15 17
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 32 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 17 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I8 TCGA-EE-A29H TCGA-EE-A29M 
       22.55        25.15         4.41        27.12 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       32.55        70.16        98.76        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-DA-A3F8 
       13.68         9.99        44.52        36.69        17.56        14.83 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 TCGA-ER-A19J TCGA-FS-A1ZR 
       38.63        12.03         6.48         8.94         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              4.41               4.18 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             27.12              98.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            23.850             14.255 
[1] "4.4 - 27.1 (23.9)" "4.2 - 98.8 (14.3)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D66V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                    0             1
  19Q LOSS WILD-TYPE                  6             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q LOSS MUTATED                                                                                          2
  19Q LOSS WILD-TYPE                                                                                       10
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                     5
  19Q LOSS WILD-TYPE                  43
D66V3, multiclass
                                                                                          clus
vv                                                                                         19Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 10
  REGIONAL LYMPH NODE                                                                                      43
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    4
  19Q LOSS WILD-TYPE   18   41
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  4                 41
                    vv
clus                 M0 M1 M1A M1B M1C
  19Q LOSS MUTATED    4  0   0   1   1
  19Q LOSS WILD-TYPE 52  1   1   0   1
D66V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  19Q LOSS MUTATED    2  0   0   0   1   0   1  2  0
  19Q LOSS WILD-TYPE 31  1   2   7   0   5   2  5  2
D66V6, multiclass
D66V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q LOSS MUTATED             0       0        1        1        0         0
  19Q LOSS WILD-TYPE           2      10        1        4        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  19Q LOSS MUTATED           0         0          0          1          1
  19Q LOSS WILD-TYPE         2         5          2          6          8
                    vv
clus                 STAGE IV
  19Q LOSS MUTATED          1
  19Q LOSS WILD-TYPE        2
D66V8, multiclass

Clustering(67) Variable = 20p loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    2  1
  20P LOSS WILD-TYPE 15 18
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 33 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 18 
$`20P LOSS MUTATED`
TCGA-EE-A29E TCGA-EE-A29P TCGA-FS-A1ZR 
       38.63        12.03         8.81 

$`20P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       10.03        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
       17.56        14.83        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A2A6 
        7.96        37.97         4.41        27.12         6.48         8.94 
TCGA-ER-A19J TCGA-GN-A262 TCGA-GN-A265 
        4.18        24.85        84.72 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              8.81               4.18 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             38.63              98.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.03              15.25 
[1] "8.8 - 38.6 (12.0)" "4.2 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    0             0
  20P LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P LOSS MUTATED                                                                                          1
  20P LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     2
  20P LOSS WILD-TYPE                  46
D67V3, multiclass
                                                                                          clus
vv                                                                                         20P LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     2
                                                                                          clus
vv                                                                                         20P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      46
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    2
  20P LOSS WILD-TYPE   21   43
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  2                 43
                    vv
clus                 M0 M1 M1A M1B M1C
  20P LOSS MUTATED    3  0   0   0   0
  20P LOSS WILD-TYPE 53  1   1   1   2
D67V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  20P LOSS MUTATED    2  0   0   1   0   0   0  0  0
  20P LOSS WILD-TYPE 31  1   2   6   1   5   3  7  2
D67V6, multiclass
D67V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P LOSS MUTATED             0       0        0        0        1         0
  20P LOSS WILD-TYPE           2      10        2        5        7         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  20P LOSS MUTATED           1         0          0          1          0
  20P LOSS WILD-TYPE         1         5          2          6          9
                    vv
clus                 STAGE IV
  20P LOSS MUTATED          0
  20P LOSS WILD-TYPE        3
D67V8, multiclass

Clustering(68) Variable = 21q loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    3  1
  21Q LOSS WILD-TYPE 14 18
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 32 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 18 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A20B TCGA-EE-A29H TCGA-EE-A2A6 
       32.55        36.07         4.41         8.94 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        98.76        22.55        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
       15.25        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       14.83        12.20         5.13         8.81         7.96        37.97 
TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J TCGA-FS-A1ZR 
       38.63        27.12        12.03         6.48         4.18         8.81 
TCGA-GN-A262 TCGA-GN-A265 
       24.85        84.72 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              4.41               4.18 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             36.07              98.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            20.745             15.040 
[1] "4.4 - 36.1 (20.7)" "4.2 - 98.8 (15.0)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D68V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    0             0
  21Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          1
  21Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                     7
  21Q LOSS WILD-TYPE                  41
D68V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      41
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    5
  21Q LOSS WILD-TYPE   19   40
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  5                 40
                    vv
clus                 M0 M1 M1A M1B M1C
  21Q LOSS MUTATED    8  0   0   0   0
  21Q LOSS WILD-TYPE 48  1   1   1   2
D68V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  21Q LOSS MUTATED    7  0   1   0   0   0   0  0  0
  21Q LOSS WILD-TYPE 26  1   1   7   1   5   3  7  2
D68V6, multiclass
D68V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q LOSS MUTATED             1       1        2        0        3         0
  21Q LOSS WILD-TYPE           1       9        0        5        5         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  21Q LOSS MUTATED           0         0          1          0          0
  21Q LOSS WILD-TYPE         2         5          1          7          9
                    vv
clus                 STAGE IV
  21Q LOSS MUTATED          0
  21Q LOSS WILD-TYPE        3
D68V8, multiclass

Clustering(69) Variable = 22q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    2  1
  22Q LOSS WILD-TYPE 15 18
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 33 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 18 
$`22Q LOSS MUTATED`
TCGA-DA-A1I2 TCGA-EE-A29C TCGA-EE-A2A6 
       13.68        37.97         8.94 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY 
        6.35        15.25        13.32         9.30        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       10.03         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-ER-A19J 
       38.63         4.41        27.12        12.03         6.48         4.18 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A265 
        8.81        24.85        84.72 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              8.94               4.18 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             37.97              98.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.68              15.25 
[1] "8.9 - 38.0 (13.7)" "4.2 - 98.8 (15.2)"
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q5         TCGA-D3-A1Q6         TCGA-D3-A1Q7 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q9         TCGA-D3-A2J9         TCGA-D3-A2JD 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JK         TCGA-D3-A3C6         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-DA-A1HW         TCGA-DA-A1HY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I0         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F5         TCGA-DA-A3F8         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A20H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29A         TCGA-EE-A29C         TCGA-EE-A29E 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29H         TCGA-EE-A29M         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A2A6         TCGA-ER-A19J 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-GN-A262         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D69V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    0             0
  22Q LOSS WILD-TYPE                  6             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q LOSS MUTATED                                                                                          1
  22Q LOSS WILD-TYPE                                                                                       11
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                     3
  22Q LOSS WILD-TYPE                  45
D69V3, multiclass
                                                                                          clus
vv                                                                                         22Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                        6
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 11
  REGIONAL LYMPH NODE                                                                                      45
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    3
  22Q LOSS WILD-TYPE   21   42
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  3                 42
                    vv
clus                 M0 M1 M1A M1B M1C
  22Q LOSS MUTATED    4  0   0   0   0
  22Q LOSS WILD-TYPE 52  1   1   1   2
D69V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2A N2B N2C N3 NX
  22Q LOSS MUTATED    3  0   0   0   0   1   0  0  0
  22Q LOSS WILD-TYPE 30  1   2   7   1   4   3  7  2
D69V6, multiclass
D69V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       1        1        1        0         0
  22Q LOSS WILD-TYPE           2       9        1        4        8         3
                    vv
clus                 STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  22Q LOSS MUTATED           0         0          0          0          1
  22Q LOSS WILD-TYPE         2         5          2          7          8
                    vv
clus                 STAGE IV
  22Q LOSS MUTATED          0
  22Q LOSS WILD-TYPE        3
D69V8, multiclass

Clustering(70) Variable = Xq loss mutation analysis
D70V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 15 18
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                33 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                18 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29H TCGA-GN-A262 
       15.25         4.41        24.85 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        70.16        98.76        22.55        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CE TCGA-D3-A3MO TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        6.35        13.32         9.30        35.80        51.12        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F5 
       13.68         9.99        44.52        36.69        25.15        17.56 
TCGA-DA-A3F8 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       14.83        12.20        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A6 
       37.97        38.63        27.12        12.03         6.48         8.94 
TCGA-ER-A19J TCGA-FS-A1ZR TCGA-GN-A265 
        4.18         8.81        84.72 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.41              4.18 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            24.85             98.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            15.25             14.83 
[1] "4.4 - 24.9 (15.2)" "4.2 - 98.8 (14.8)"
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7        TCGA-D3-A1Q9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-D3-A3CE        TCGA-D3-A3MO        TCGA-DA-A1HW        TCGA-DA-A1HY 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I0        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A3F5        TCGA-DA-A3F8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A20B        TCGA-EE-A20F        TCGA-EE-A20H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29E        TCGA-EE-A29H 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29T        TCGA-EE-A2A6 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-FS-A1ZR        TCGA-GN-A262        TCGA-GN-A265 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D70V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                    1             0
  XQ LOSS WILD-TYPE                  5             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ LOSS MUTATED                                                                                          1
  XQ LOSS WILD-TYPE                                                                                       11
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                     2
  XQ LOSS WILD-TYPE                  46
D70V3, multiclass
                                                                                          clus
vv                                                                                         XQ LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       5
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                11
  REGIONAL LYMPH NODE                                                                                     46
D70V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    1
  XQ LOSS WILD-TYPE   19   44
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 1                44
                   vv
clus                M0 M1 M1A M1B M1C
  XQ LOSS MUTATED    3  0   0   0   0
  XQ LOSS WILD-TYPE 53  1   1   1   2
D70V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2A N2B N2C N3 NX
  XQ LOSS MUTATED    3  0   0   0   0   0   0  0  0
  XQ LOSS WILD-TYPE 30  1   2   7   1   5   3  7  2
D70V6, multiclass
D70V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ LOSS MUTATED             1       0        1        1        0         0
  XQ LOSS WILD-TYPE           1      10        1        4        8         3
                   vv
clus                STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  XQ LOSS MUTATED           0         0          0          0          0
  XQ LOSS WILD-TYPE         2         5          2          7          9
                   vv
clus                STAGE IV
  XQ LOSS MUTATED          0
  XQ LOSS WILD-TYPE        3
D70V8, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"      "DISTANT.METASTASIS"   "LYMPH.NODE.METASTASIS" 
                       V7                        V8 
        "TUMOR.STAGECODE"   "NEOPLASM.DISEASESTAGE" 
> q(save="no")
