
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-Regional_Metastatic/3164440/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-Regional_Metastatic/3215668/SKCM-Regional_Metastatic.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-Regional_Metastatic", "-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-Regional_Metastatic"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=152, in cluster file=147, common to both=147
[1] "Reduce the number of clustering variables from 80 to 73."
[1]  73 147
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               127 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               127 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               48                99 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               48                99 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               16               131 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               16               131 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               132 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               15               132 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               135 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               12               135 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15               132 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15               132 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               133 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               133 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               135 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               135 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               13               134 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               13               134 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               142 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5               142 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               45               102 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               45               102 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               138 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               138 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               63                84 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               63                84 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62                85 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62                85 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               29               118 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               29               118 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               46               101 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               46               101 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               144 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               144 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               144 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               144 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                138 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 9                138 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                141 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                141 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                131 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                16                131 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                140 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                140 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                126 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                126 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                135 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                135 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                126 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                126 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                135 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                12                135 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                137 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                10                137 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                134 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                134 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                21                126 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                21                126 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                128 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                19                128 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                137 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                137 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                140 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                140 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                136 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                136 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                104 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                43                104 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                 94 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                 94 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                17                130 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                17                130 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                37                110 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                37                110 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               135 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12               135 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               143 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4               143 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               133 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               133 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               134 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               13               134 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               137 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10               137 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               135 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               135 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15               132 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               15               132 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               131 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16               131 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               18               129 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               18               129 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31               116 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               31               116 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               136 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               136 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               53                94 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               53                94 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               131 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16               131 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82                65 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               82                65 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               61                86 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               61                86 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                 83 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                64                 83 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                71                 76 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                71                 76 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                35                112 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                35                112 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                39                108 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                39                108 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                139 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                139 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                132 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                15                132 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                124 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                124 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                112 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                112 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                135 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                12                135 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                138 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                138 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                127 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                127 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                114 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                114 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                135 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                135 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                26                121 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                26                121 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                123 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                24                123 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                133 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                133 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                132 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                15                132 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                141 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                141 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                129 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                18                129 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                135 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                12                135 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               143 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4               143 
[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 147 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
          NA           NA           NA         3004           NA           NA 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
          NA           NA           NA           NA           NA           NA 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A148 
        1390           NA           NA           NA          164           NA 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
          NA           NA           NA          122           87         1484 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
          NA         1555           NA         1192           NA           NA 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        1116           NA          680           NA          589           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
         534          451           NA           NA           NA           NA 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
          NA         1097          156         1155           NA         1175 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
         134           NA           NA          366          247          269 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
         304          197           NA           NA          769          727 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE 
          NA          272           NA           NA           NA           NA 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
          NA           NA           NA           NA           NA         1303 
TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
          NA         2386          200           52          181         2195 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZD TCGA-FS-A1ZG 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZR TCGA-FS-A1ZS 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
          NA         1637          328          195           31           NA 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
          NA          756           NA         2577           NA           NA 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA          447 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=77,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "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 
  6   4  11   3  15  14   6   4  19  10   4   7  20   1  10 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 147 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=10, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    4  7
  1P GAIN WILD-TYPE 35 37
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11                72 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                37 
$`1P GAIN MUTATED`
TCGA-D3-A2J8 TCGA-DA-A1IC TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A2A2 
        8.38         6.64        11.15        38.63         1.08        23.90 
TCGA-ER-A19F TCGA-ER-A3ET TCGA-FR-A3YN TCGA-GN-A266 TCGA-GN-A26A 
       11.11         6.58         5.95        10.09        12.16 

$`1P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       10.26        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99        36.69        25.15        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29N 
        4.27        36.07         5.13        37.97         4.41         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
       12.03         8.12         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19J 
       11.31        25.28         9.67         8.94         3.52         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         1.71        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       24.85        31.33        84.72        16.21        15.39        14.70 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.08              1.02 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            38.63             98.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            10.09             13.50 
[1] "1.1 - 38.6 (10.1)" "1.0 - 98.8 (13.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7   13
  1P GAIN WILD-TYPE   28   99
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                28
  REGIONAL LYMPH NODE                                                                                     99
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      7   13
  1P GAIN WILD-TYPE   45   82
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               7                45
  MALE                13                82
                   vv
clus                 M0  M1 M1A M1B M1C
  1P GAIN MUTATED    19   0   0   0   0
  1P GAIN WILD-TYPE 109   1   2   2   1
D1V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P GAIN MUTATED   10  0   3   3  0   1   0   1  1  0
  1P GAIN WILD-TYPE 67  2   3   9  1   3  11   3 15  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       1        3        3        1         0
  1P GAIN WILD-TYPE           1      15        5       10       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P GAIN MUTATED           0         1         0          3          4
  1P GAIN WILD-TYPE         8         3         8          2         12
                   vv
clus                STAGE IIIC STAGE IV
  1P GAIN MUTATED            2        0
  1P GAIN WILD-TYPE         19        4
D1V8, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   15 16
  1Q GAIN WILD-TYPE 24 28
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31                52 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                28 
$`1Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J8 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV 
       16.47         8.38        11.41        13.32         9.30         5.39 
TCGA-D9-A3Z3 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EE-A17Z 
        2.86        39.19         9.99         6.64         7.00         6.31 
TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S 
       36.07        11.15        38.63         1.08         8.84         9.99 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A3ET 
       25.28        23.90         8.94         3.52        11.11         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        1.71         5.95        72.16        10.09        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`1Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A3Z1 
       21.14         6.35        15.25        45.70        24.00         4.01 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 
       48.79        35.80        51.12        10.03        13.68        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       25.15        22.36        19.36        17.56        14.83        11.57 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29H 
        1.12        12.20         4.27         5.13        37.97         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         8.12         6.48         8.09        11.31 
TCGA-EE-A2A5 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        9.67         4.18        12.99        28.64        42.84        78.44 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A268 
       24.85        31.33        84.72        15.39 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.08              1.02 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.16             98.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             9.99             15.30 
[1] "1.1 - 72.2 (10.0)" "1.0 - 98.8 (15.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15   33
  1Q GAIN WILD-TYPE   20   79
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              15
  REGIONAL LYMPH NODE                                                                                   33
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                20
  REGIONAL LYMPH NODE                                                                                     79
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     15   33
  1Q GAIN WILD-TYPE   37   62
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              15                37
  MALE                33                62
                   vv
clus                M0 M1 M1A M1B M1C
  1Q GAIN MUTATED   43  0   1   0   0
  1Q GAIN WILD-TYPE 85  1   1   2   1
D2V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q GAIN MUTATED   25  0   3   7  0   3   2   2  3  0
  1Q GAIN WILD-TYPE 52  2   3   5  1   1   9   2 13  2
D2V6, multiclass
D2V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q GAIN MUTATED             0       2        4        6        5         2
  1Q GAIN WILD-TYPE           1      14        4        7       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED           2         2         2          4          7
  1Q GAIN WILD-TYPE         6         2         6          1          9
                   vv
clus                STAGE IIIC STAGE IV
  1Q GAIN MUTATED            6        1
  1Q GAIN WILD-TYPE         15        3
D2V8, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    6  6
  2P GAIN WILD-TYPE 33 38
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12                71 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                38 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EE-A29D 
       16.47        70.16        22.55        11.41         5.39        11.15 
TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A6 TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A 
        1.08         8.84         8.94        42.84         5.95        72.16 

$`2P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
        6.35        15.25        45.70        13.32        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.86        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       37.97        38.63         4.41         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        9.67         3.52        11.11         4.18        12.99        28.64 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
       78.44         6.58         1.71         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.08              1.02 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.16             98.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            11.28             12.20 
[1] "1.1 - 72.2 (11.3)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   11
  2P GAIN WILD-TYPE   30  101
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   11
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    101
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   11
  2P GAIN WILD-TYPE   47   84
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5                47
  MALE                11                84
                   vv
clus                 M0  M1 M1A M1B M1C
  2P GAIN MUTATED    15   0   0   0   0
  2P GAIN WILD-TYPE 113   1   2   2   1
D3V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P GAIN MUTATED    7  0   0   4  0   2   0   0  2  0
  2P GAIN WILD-TYPE 70  2   6   8  1   2  11   4 14  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       0        2        1        1         2
  2P GAIN WILD-TYPE           1      16        6       12       16         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P GAIN MUTATED           0         1         1          0          2
  2P GAIN WILD-TYPE         8         3         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  2P GAIN MUTATED            5        0
  2P GAIN WILD-TYPE         16        4
D3V8, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    6  5
  2Q GAIN WILD-TYPE 33 39
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11                72 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                39 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EE-A29L 
       16.47        70.16        22.55        11.41         5.39         1.08 
TCGA-EE-A29R TCGA-EE-A2A6 TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A 
        8.84         8.94        42.84         5.95        72.16 

$`2Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
        6.35        15.25        45.70        13.32        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.86        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         4.41         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.12         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       23.90         9.67         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 
       28.64        78.44         6.58         1.71         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        16.21        15.39        12.16        14.70 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.08              1.02 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            72.16             98.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            11.41             12.18 
[1] "1.1 - 72.2 (11.4)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   10
  2Q GAIN WILD-TYPE   30  102
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    102
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   10
  2Q GAIN WILD-TYPE   47   85
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                47
  MALE                10                85
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q GAIN MUTATED    14   0   0   0   0
  2Q GAIN WILD-TYPE 114   1   2   2   1
D4V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q GAIN MUTATED    7  0   0   3  0   2   0   0  2  0
  2Q GAIN WILD-TYPE 70  2   6   9  1   2  11   4 14  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       0        2        1        1         2
  2Q GAIN WILD-TYPE           1      16        6       12       16         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED           0         1         1          0          2
  2Q GAIN WILD-TYPE         8         3         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  2Q GAIN MUTATED            4        0
  2Q GAIN WILD-TYPE         17        4
D4V8, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    5  4
  3P GAIN WILD-TYPE 34 40
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                9                74 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                40 
$`3P GAIN MUTATED`
TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29T 
        5.39         7.00        17.56         1.08         8.84         6.48 
TCGA-ER-A3ET TCGA-GN-A264 TCGA-GN-A266 
        6.58        31.33        10.09 

$`3P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        13.32        24.00         9.30         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         8.12         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL 
        4.18        12.99        28.64        42.84        78.44         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
        1.02        15.35        24.85        84.72        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              1.02 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            31.33             98.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            7.000            13.155 
[1] "1.1 - 31.3 (7.0)"  "1.0 - 98.8 (13.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    7
  3P GAIN WILD-TYPE   30  105
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    105
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5    7
  3P GAIN WILD-TYPE   47   88
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               5                47
  MALE                 7                88
                   vv
clus                 M0  M1 M1A M1B M1C
  3P GAIN MUTATED    10   0   0   0   0
  3P GAIN WILD-TYPE 118   1   2   2   1
D5V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P GAIN MUTATED    2  0   2   1  0   1   1   0  2  1
  3P GAIN WILD-TYPE 75  2   4  11  1   3  10   4 14  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       0        1        0        0         1
  3P GAIN WILD-TYPE           1      16        7       13       17         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P GAIN MUTATED           0         0         0          1          3
  3P GAIN WILD-TYPE         8         4         8          4         13
                   vv
clus                STAGE IIIC STAGE IV
  3P GAIN MUTATED            3        0
  3P GAIN WILD-TYPE         18        4
D5V8, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    6  4
  3Q GAIN WILD-TYPE 33 40
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               10                73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                40 
$`3Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29R TCGA-EE-A29T 
        5.39         7.00        17.56         5.13         8.84         6.48 
TCGA-ER-A19M TCGA-ER-A3ET TCGA-GN-A266 TCGA-GN-A26A 
       28.64         6.58        10.09        12.16 

$`3Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        13.32        24.00         9.30         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       36.07        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         8.12         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A3YN 
        4.18        12.99        42.84        78.44         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.35        24.85        31.33        84.72        16.21        15.39 
TCGA-GN-A26D 
       14.70 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5.13              1.02 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            28.64             98.76 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             7.92             13.32 
[1] "5.1 - 28.6 (7.9)"  "1.0 - 98.8 (13.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    9
  3Q GAIN WILD-TYPE   29  103
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                    103
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    9
  3Q GAIN WILD-TYPE   46   86
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               6                46
  MALE                 9                86
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q GAIN MUTATED    14   0   0   0   0
  3Q GAIN WILD-TYPE 114   1   2   2   1
D6V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q GAIN MUTATED    6  0   3   1  0   1   1   0  1  1
  3Q GAIN WILD-TYPE 71  2   3  11  1   3  10   4 15  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        1        1        2         1
  3Q GAIN WILD-TYPE           1      15        7       12       15         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q GAIN MUTATED           0         0         0          2          3
  3Q GAIN WILD-TYPE         8         4         8          3         13
                   vv
clus                STAGE IIIC STAGE IV
  3Q GAIN MUTATED            2        0
  3Q GAIN WILD-TYPE         19        4
D6V8, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    7  2
  4P GAIN WILD-TYPE 32 42
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9                74 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                42 
$`4P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EE-A29P TCGA-ER-A3ET 
       13.32        48.79        39.19        17.56        12.03         6.58 
TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A26D 
        5.95        31.33        14.70 

$`4P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47         8.12         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       11.31        25.28        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        1.71        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        1.02        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A 
       15.39        12.16 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.95              1.02 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            48.79             98.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.70             11.49 
[1] "6.0 - 48.8 (14.7)" "1.0 - 98.8 (11.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr=" "3.1"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   10
  4P GAIN WILD-TYPE   31  102
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    102
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    8
  4P GAIN WILD-TYPE   46   87
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6                46
  MALE                 8                87
                   vv
clus                 M0  M1 M1A M1B M1C
  4P GAIN MUTATED    12   0   0   0   0
  4P GAIN WILD-TYPE 116   1   2   2   1
D7V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P GAIN MUTATED    5  0   3   1  0   0   1   1  2  0
  4P GAIN WILD-TYPE 72  2   3  11  1   4  10   3 14  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       1        1        1        0         0
  4P GAIN WILD-TYPE           1      15        7       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P GAIN MUTATED           0         2         2          2          2
  4P GAIN WILD-TYPE         8         2         6          3         14
                   vv
clus                STAGE IIIC STAGE IV
  4P GAIN MUTATED            2        0
  4P GAIN WILD-TYPE         19        4
D7V8, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    6  3
  4Q GAIN WILD-TYPE 33 41
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9                74 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                41 
$`4Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EE-A29D TCGA-EE-A29P 
       13.32        48.79        39.19        17.56        11.15        12.03 
TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A26D 
        5.95        31.33        14.70 

$`4Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        1.71        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        1.02        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A 
       15.39        12.16 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             5.95              1.02 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            48.79             98.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            14.70             11.49 
[1] "6.0 - 48.8 (14.7)" "1.0 - 98.8 (11.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "hr=" "2.1"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2   10
  4Q GAIN WILD-TYPE   33  102
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    102
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    8
  4Q GAIN WILD-TYPE   48   87
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4                48
  MALE                 8                87
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q GAIN MUTATED     9   0   0   0   0
  4Q GAIN WILD-TYPE 119   1   2   2   1
D8V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q GAIN MUTATED    3  0   2   2  0   0   1   0  2  0
  4Q GAIN WILD-TYPE 74  2   4  10  1   4  10   4 14  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        1        0         0
  4Q GAIN WILD-TYPE           1      16        8       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q GAIN MUTATED           0         2         1          1          2
  4Q GAIN WILD-TYPE         8         2         7          4         14
                   vv
clus                STAGE IIIC STAGE IV
  4Q GAIN MUTATED            3        0
  4Q GAIN WILD-TYPE         18        4
D8V8, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    1  4
  5P GAIN WILD-TYPE 38 40
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                78 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                40 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JK TCGA-EE-A29T TCGA-EE-A2A0 TCGA-ER-A19M 
       32.55         6.35         6.48        11.31        28.64 

$`5P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        9.99         8.09        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        12.99        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        16.21        15.39        12.16        14.70 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             6.35              1.02 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            32.55             98.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            11.31             12.18 
[1] "6.3 - 32.5 (11.3)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5P GAIN WILD-TYPE" "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5P GAIN WILD-TYPE" "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5P GAIN WILD-TYPE" "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   12
  5P GAIN WILD-TYPE   34  100
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    100
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    8
  5P GAIN WILD-TYPE   47   87
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               5                47
  MALE                 8                87
                   vv
clus                 M0  M1 M1A M1B M1C
  5P GAIN MUTATED    12   0   0   1   0
  5P GAIN WILD-TYPE 116   1   2   1   1
D9V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P GAIN MUTATED    8  0   0   1  0   1   1   0  1  1
  5P GAIN WILD-TYPE 69  2   6  11  1   3  10   4 15  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       2        1        1        1         1
  5P GAIN WILD-TYPE           0      14        7       12       16         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P GAIN MUTATED           0         1         0          0          1
  5P GAIN WILD-TYPE         8         3         8          5         15
                   vv
clus                STAGE IIIC STAGE IV
  5P GAIN MUTATED            1        0
  5P GAIN WILD-TYPE         20        4
D9V8, multiclass

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN WILD-TYPE 39 44
5Q GAIN WILD-TYPE 
               83 
[1] 44
$`5Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       45.70        13.32        24.00         9.30         5.39         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.86        48.79        35.80        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       19.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
        1.12        12.20         4.27        36.07         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

5Q GAIN WILD-TYPE 
             1.02 
5Q GAIN WILD-TYPE 
            98.76 
5Q GAIN WILD-TYPE 
            12.16 
[1] "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    5
  5Q GAIN WILD-TYPE   35  107
                                                                                          clus
vv                                                                                         5Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         5Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    107
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    3
  5Q GAIN WILD-TYPE   50   92
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                50
  MALE                 3                92
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q GAIN MUTATED     5   0   0   0   0
  5Q GAIN WILD-TYPE 123   1   2   2   1
D10V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q GAIN MUTATED    4  0   0   0  0   1   0   0  0  0
  5Q GAIN WILD-TYPE 73  2   6  12  1   3  11   4 16  2
D10V6, multiclass
D10V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q GAIN MUTATED             0       1        1        0        1         1
  5Q GAIN WILD-TYPE           1      15        7       13       16         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q GAIN MUTATED           0         0         0          0          0
  5Q GAIN WILD-TYPE         8         4         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  5Q GAIN MUTATED            0        0
  5Q GAIN WILD-TYPE         21        4
D10V8, multiclass

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    7 15
  6P GAIN WILD-TYPE 32 29
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22                61 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               15                29 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1I0 
       16.47        98.76        21.14        15.25        48.79        10.03 
TCGA-DA-A1I2 TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A29P 
       13.68         7.00         6.31         1.12         4.27        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A5 TCGA-ER-A19M TCGA-ER-A19N TCGA-GN-A264 
        8.84         9.99         9.67        28.64        42.84        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        12.16        14.70 

$`6P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        70.16        28.08        22.55        10.26         8.38 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        45.70        13.32        24.00         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        5.39         4.01         2.86        35.80        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       17.56        14.83        11.57        12.20        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.12         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 
        8.94         3.52        11.11         4.18        12.99        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 
       10.78         6.41         1.02        15.35        24.85        84.72 
TCGA-GN-A268 
       15.39 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.12              1.02 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            98.76             84.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            12.92             11.57 
[1] "1.1 - 98.8 (12.9)" "1.0 - 84.7 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
[1] "hr=" "1.4"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9   36
  6P GAIN WILD-TYPE   26   76
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   36
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                26
  REGIONAL LYMPH NODE                                                                                     76
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     20   25
  6P GAIN WILD-TYPE   32   70
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              20                32
  MALE                25                70
                   vv
clus                M0 M1 M1A M1B M1C
  6P GAIN MUTATED   38  0   1   0   0
  6P GAIN WILD-TYPE 90  1   1   2   1
D11V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P GAIN MUTATED   24  0   4   3  0   2   3   0  4  0
  6P GAIN WILD-TYPE 53  2   2   9  1   2   8   4 12  2
D11V6, multiclass
D11V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P GAIN MUTATED             0       5        1        5        5         3
  6P GAIN WILD-TYPE           1      11        7        8       12         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P GAIN MUTATED           3         2         0          4          4
  6P GAIN WILD-TYPE         5         2         8          1         12
                   vv
clus                STAGE IIIC STAGE IV
  6P GAIN MUTATED            6        0
  6P GAIN WILD-TYPE         15        4
D11V8, multiclass

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    2  2
  6Q GAIN WILD-TYPE 37 42
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4                79 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                42 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-DA-A1I0 TCGA-EE-A29R TCGA-ER-A19M 
       98.76        10.03         8.84        28.64 

$`6Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        70.16        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
        8.94         3.52        11.11         4.18        12.99        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR 
       78.44         6.58         1.71         5.95        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.09        16.21        15.39        12.16 
TCGA-GN-A26D 
       14.70 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             8.84              1.02 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            98.76             84.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           19.335            12.160 
[1] "8.8 - 98.8 (19.3)" "1.0 - 84.7 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    7
  6Q GAIN WILD-TYPE   33  105
                                                                                          clus
vv                                                                                         6Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         6Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    105
D12V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4    5
  6Q GAIN WILD-TYPE   48   90
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4                48
  MALE                 5                90
                   vv
clus                 M0  M1 M1A M1B M1C
  6Q GAIN MUTATED     8   0   1   0   0
  6Q GAIN WILD-TYPE 120   1   1   2   1
D12V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q GAIN MUTATED    6  0   0   2  0   0   0   0  1  0
  6Q GAIN WILD-TYPE 71  2   6  10  1   4  11   4 15  2
D12V6, multiclass
D12V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q GAIN MUTATED             0       0        0        3        1         1
  6Q GAIN WILD-TYPE           1      16        8       10       16         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q GAIN MUTATED           1         0         0          0          0
  6Q GAIN WILD-TYPE         7         4         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  6Q GAIN MUTATED            2        0
  6Q GAIN WILD-TYPE         19        4
D12V8, multiclass

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   12 21
  7P GAIN WILD-TYPE 27 23
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               33                50 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               21                23 
$`7P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO 
       16.47        32.55        70.16        22.55        11.41         9.30 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        2.86        48.79        51.12        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D 
       36.69        25.15         6.64         1.12        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 
       38.63         9.47        12.03         6.48        11.31         8.94 
TCGA-ER-A19J TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-GN-A264 TCGA-GN-A266 
        4.18         1.71         5.95         8.81        31.33        10.09 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        12.16        14.70 

$`7P GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       98.76        28.08        10.26         8.38        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        13.32        24.00         5.39         4.01 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       35.80        39.19        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       14.83        11.57         6.31        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        5.13         4.41         1.08         8.12         8.84         9.99 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F 
        8.09        25.28        23.90         9.67         3.52        11.11 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A 
       12.99        28.64        42.84        78.44         6.58        72.16 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A265 TCGA-GN-A268 
       84.72        15.39 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1.12              1.02 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            70.16             98.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           11.410            13.155 
[1] "1.1 - 70.2 (11.4)" "1.0 - 98.8 (13.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     19   44
  7P GAIN WILD-TYPE   16   68
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              19
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                16
  REGIONAL LYMPH NODE                                                                                     68
D13V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     19   44
  7P GAIN WILD-TYPE   33   51
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              19                33
  MALE                44                51
                   vv
clus                M0 M1 M1A M1B M1C
  7P GAIN MUTATED   53  1   2   0   1
  7P GAIN WILD-TYPE 75  0   0   2   0
D13V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7P GAIN MUTATED   29  0   4   8  0   2   4   4  5  2
  7P GAIN WILD-TYPE 48  2   2   4  1   2   7   0 11  0
D13V6, multiclass
D13V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P GAIN MUTATED             1       5        5        2        8         3
  7P GAIN WILD-TYPE           0      11        3       11        9         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P GAIN MUTATED           0         3         3          4          9
  7P GAIN WILD-TYPE         8         1         5          1          7
                   vv
clus                STAGE IIIC STAGE IV
  7P GAIN MUTATED            8        3
  7P GAIN WILD-TYPE         13        1
D13V8, multiclass

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   15 20
  7Q GAIN WILD-TYPE 24 24
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               35                48 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               20                24 
$`7Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MO 
       16.47        32.55        70.16        22.55        11.41         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        5.39         2.86        48.79        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-DA-A3F8 
        9.99        36.69        25.15         6.64        17.56        14.83 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P 
        1.12        12.20        37.97        38.63         9.47        12.03 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A3PL TCGA-FR-A3YN 
        6.48        11.31         8.94         4.18         1.71         5.95 
TCGA-FS-A1ZR TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        8.81        31.33        16.21        12.16        14.70 

$`7Q GAIN WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK 
       98.76        28.08        10.26         8.38        21.14         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HW 
       15.25        45.70        13.32        24.00         4.01        35.80 
TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EE-A17X TCGA-EE-A17Z 
       39.19        22.36        19.36         7.00        11.57         6.31 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        4.27        36.07         5.13        11.15         4.41         1.08 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.12         8.84         9.99         8.09        25.28        23.90 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        9.67         3.52        11.11        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       78.44         6.58        72.16        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
        1.02        15.35        24.85        84.72        10.09        15.39 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1.12              1.02 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.16             98.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            12.16             12.28 
[1] "1.1 - 70.2 (12.2)" "1.0 - 98.8 (12.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18   44
  7Q GAIN WILD-TYPE   17   68
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              18
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                17
  REGIONAL LYMPH NODE                                                                                     68
D14V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     20   42
  7Q GAIN WILD-TYPE   32   53
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              20                32
  MALE                42                53
                   vv
clus                M0 M1 M1A M1B M1C
  7Q GAIN MUTATED   54  1   2   0   1
  7Q GAIN WILD-TYPE 74  0   0   2   0
D14V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7Q GAIN MUTATED   28  0   4   7  0   3   5   4  6  2
  7Q GAIN WILD-TYPE 49  2   2   5  1   1   6   0 10  0
D14V6, multiclass
D14V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q GAIN MUTATED             1       5        4        2        9         2
  7Q GAIN WILD-TYPE           0      11        4       11        8         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED           0         3         3          4         11
  7Q GAIN WILD-TYPE         8         1         5          1          5
                   vv
clus                STAGE IIIC STAGE IV
  7Q GAIN MUTATED            8        3
  7Q GAIN WILD-TYPE         13        1
D14V8, multiclass

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    8 11
  8P GAIN WILD-TYPE 31 33
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               19                64 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                33 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I1 
       70.16        45.70        13.32         5.39        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29R TCGA-ER-A19J 
       13.68         9.99        17.56         1.12         8.84         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-FS-A1ZR TCGA-GN-A267 TCGA-GN-A26A 
       12.99        28.64        42.84         8.81        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`8P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
        8.38        21.14        11.41         6.35        15.25        24.00 
TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 
        9.30         4.01         2.86        48.79        35.80        10.03 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       14.83        11.57         6.31        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.12         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       11.31        25.28        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       11.11        78.44         6.58         1.71         5.95        72.16 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       31.33        84.72        10.09        15.39 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.12              1.02 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.16             98.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            13.68             11.36 
[1] "1.1 - 70.2 (13.7)" "1.0 - 98.8 (11.4)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11   18
  8P GAIN WILD-TYPE   24   94
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              11
  REGIONAL LYMPH NODE                                                                                   18
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                24
  REGIONAL LYMPH NODE                                                                                     94
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   20
  8P GAIN WILD-TYPE   43   75
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9                43
  MALE                20                75
                   vv
clus                 M0  M1 M1A M1B M1C
  8P GAIN MUTATED    24   1   0   0   0
  8P GAIN WILD-TYPE 104   0   2   2   1
D15V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P GAIN MUTATED   12  0   3   4  0   1   2   0  4  0
  8P GAIN WILD-TYPE 65  2   3   8  1   3   9   4 12  2
D15V6, multiclass
D15V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P GAIN MUTATED             0       1        0        2        4         2
  8P GAIN WILD-TYPE           1      15        8       11       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P GAIN MUTATED           0         3         2          2          3
  8P GAIN WILD-TYPE         8         1         6          3         13
                   vv
clus                STAGE IIIC STAGE IV
  8P GAIN MUTATED            6        1
  8P GAIN WILD-TYPE         15        3
D15V8, multiclass

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   11 19
  8Q GAIN WILD-TYPE 28 25
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               30                53 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               19                25 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CE 
       16.47        70.16        22.55        10.26        45.70        13.32 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        9.30         5.39        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A29E 
        9.99         7.00        17.56         6.31         1.12        38.63 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        8.84         6.48         9.67         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A3ET TCGA-FS-A1ZR TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       42.84         6.58         8.81        16.21        12.16        14.70 

$`8Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       32.55        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
        6.35        15.25        24.00         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       35.80        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
       14.83        11.57        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15         4.41         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.12         9.99         8.09        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A3YN 
        8.94         3.52        11.11        78.44         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
       72.16        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        15.39 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.12              1.02 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            70.16             98.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           12.575            12.030 
[1] "1.1 - 70.2 (12.6)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
[1] "hr=" "1.4"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     15   31
  8Q GAIN WILD-TYPE   20   81
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              15
  REGIONAL LYMPH NODE                                                                                   31
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                20
  REGIONAL LYMPH NODE                                                                                     81
D16V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     13   33
  8Q GAIN WILD-TYPE   39   62
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              13                39
  MALE                33                62
                   vv
clus                M0 M1 M1A M1B M1C
  8Q GAIN MUTATED   39  1   1   0   0
  8Q GAIN WILD-TYPE 89  0   1   2   1
D16V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q GAIN MUTATED   19  0   4   5  0   3   3   1  6  1
  8Q GAIN WILD-TYPE 58  2   2   7  1   1   8   3 10  1
D16V6, multiclass
D16V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q GAIN MUTATED             0       3        0        4        5         2
  8Q GAIN WILD-TYPE           1      13        8        9       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED           2         3         3          3          6
  8Q GAIN WILD-TYPE         6         1         5          2         10
                   vv
clus                STAGE IIIC STAGE IV
  8Q GAIN MUTATED            8        1
  8Q GAIN WILD-TYPE         13        3
D16V8, multiclass

Clustering(17) Variable = 9p gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    1  1
  9P GAIN WILD-TYPE 38 43
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                81 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                43 
$`9P GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-ER-A3ET 
       22.55         6.58 

$`9P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A3YN 
       12.99        28.64        42.84        78.44         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.35        24.85        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             6.58              1.02 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.55             98.76 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           14.565            12.160 
[1] "6.6 - 22.6 (14.6)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                81 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO        TCGA-D3-A3MV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV        TCGA-DA-A1HW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B        TCGA-EE-A20F 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4F0        TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3R5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"9P GAIN WILD-TYPE" 
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1    2
  9P GAIN WILD-TYPE   34  110
                                                                                          clus
vv                                                                                         9P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         9P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    110
D17V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   50   94
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                50
  MALE                 1                94
                   vv
clus                 M0  M1 M1A M1B M1C
  9P GAIN MUTATED     3   0   0   0   0
  9P GAIN WILD-TYPE 125   1   2   2   1
D17V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9P GAIN MUTATED    1  0   1   0  0   1   0   0  0  0
  9P GAIN WILD-TYPE 76  2   5  12  1   3  11   4 16  2
D17V6, multiclass
D17V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P GAIN MUTATED             0       1        0        0        0         0
  9P GAIN WILD-TYPE           1      15        8       13       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P GAIN MUTATED           0         0         0          1          1
  9P GAIN WILD-TYPE         8         4         8          4         15
                   vv
clus                STAGE IIIC STAGE IV
  9P GAIN MUTATED            0        0
  9P GAIN WILD-TYPE         21        4
D17V8, multiclass

Clustering(18) Variable = 9q gain mutation analysis
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    1  1
  9Q GAIN WILD-TYPE 38 43
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                81 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                43 
$`9Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-FR-A44A 
       22.55        72.16 

$`9Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
        5.95         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.35        24.85        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            22.55              1.02 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            72.16             98.76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           47.355            12.030 
[1] "22.6 - 72.2 (47.4)" "1.0 - 98.8 (12.0)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                81 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A2J6        TCGA-D3-A2J8        TCGA-D3-A2J9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A2JD        TCGA-D3-A2JK        TCGA-D3-A3C6        TCGA-D3-A3CC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO        TCGA-D3-A3MV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV        TCGA-DA-A1HW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1        TCGA-DA-A1I2 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B        TCGA-EE-A20F 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29X 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FS-A1ZR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4F0        TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3R5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" 
D18V2, continuous
D18V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE   35  109
                                                                                          clus
vv                                                                                         9Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         9Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    109
D18V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    1
  9Q GAIN WILD-TYPE   50   94
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                50
  MALE                 1                94
                   vv
clus                 M0  M1 M1A M1B M1C
  9Q GAIN MUTATED     3   0   0   0   0
  9Q GAIN WILD-TYPE 125   1   2   2   1
D18V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q GAIN MUTATED    2  0   0   0  0   1   0   0  0  0
  9Q GAIN WILD-TYPE 75  2   6  12  1   3  11   4 16  2
D18V6, multiclass
D18V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q GAIN MUTATED             0       1        0        0        1         0
  9Q GAIN WILD-TYPE           1      15        8       13       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q GAIN MUTATED           0         0         0          0          1
  9Q GAIN WILD-TYPE         8         4         8          5         15
                   vv
clus                STAGE IIIC STAGE IV
  9Q GAIN MUTATED            0        0
  9Q GAIN WILD-TYPE         21        4
D18V8, multiclass

Clustering(19) Variable = 11p gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 37 42
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 42 
$`11P GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EE-A29T TCGA-ER-A19N 
       13.32         7.00         6.48        42.84 

$`11P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        9.99         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        8.94         3.52        11.11         4.18        12.99        28.64 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR 
       78.44         6.58         1.71         5.95        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.09        16.21        15.39        12.16 
TCGA-GN-A26D 
       14.70 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              6.48               1.02 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             42.84              98.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.16              12.16 
[1] "6.5 - 42.8 (10.2)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11P GAIN MUTATED" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    8
  11P GAIN WILD-TYPE   34  104
                                                                                          clus
vv                                                                                         11P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     104
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    7
  11P GAIN WILD-TYPE   50   88
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 50
  MALE                  7                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  11P GAIN MUTATED     8   0   0   0   0
  11P GAIN WILD-TYPE 120   1   2   2   1
D19V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P GAIN MUTATED    3  0   2   1  0   0   1   0  0  1
  11P GAIN WILD-TYPE 74  2   4  11  1   4  10   4 16  1
D19V6, multiclass
D19V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P GAIN MUTATED             0       1        0        0        1         1
  11P GAIN WILD-TYPE           1      15        8       13       16         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED           0         0         1          1          2
  11P GAIN WILD-TYPE         8         4         7          4         14
                    vv
clus                 STAGE IIIC STAGE IV
  11P GAIN MUTATED            0        0
  11P GAIN WILD-TYPE         21        4
D19V8, multiclass

Clustering(20) Variable = 11q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE 38 42
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 80 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 42 
$`11Q GAIN MUTATED`
TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-ER-A19N 
       13.32         7.00        42.84 

$`11Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        4.41         1.08         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        9.67         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       28.64        78.44         6.58         1.71         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              7.00               1.02 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             42.84              98.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            13.320             12.095 
[1] "7.0 - 42.8 (13.3)" "1.0 - 98.8 (12.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    5
  11Q GAIN WILD-TYPE   34  107
                                                                                          clus
vv                                                                                         11Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     107
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    5
  11Q GAIN WILD-TYPE   51   90
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                1                 51
  MALE                  5                 90
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q GAIN MUTATED     5   0   0   0   0
  11Q GAIN WILD-TYPE 123   1   2   2   1
D20V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q GAIN MUTATED    2  0   1   1  0   0   1   0  0  0
  11Q GAIN WILD-TYPE 75  2   5  11  1   4  10   4 16  2
D20V6, multiclass
D20V7, 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           1      16        8       13       16         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED           0         0         1          0          2
  11Q GAIN WILD-TYPE         8         4         7          5         14
                    vv
clus                 STAGE IIIC STAGE IV
  11Q GAIN MUTATED            0        0
  11Q GAIN WILD-TYPE         21        4
D20V8, multiclass

Clustering(21) Variable = 12p gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5  8
  12P GAIN WILD-TYPE 34 36
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                13                 70 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 36 
$`12P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I7 
       16.47        70.16        22.55        13.32         5.39        36.69 
TCGA-DA-A3F5 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3PL 
       17.56         8.94         4.18        12.99        28.64         1.71 
TCGA-GN-A26A 
       12.16 

$`12P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        15.25        45.70        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        4.01         2.86        48.79        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19        13.68         9.99        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       19.36         7.00        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 
       23.90         9.67         3.52        11.11        42.84        78.44 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        6.58         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       10.09        16.21        15.39        14.70 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.71               1.02 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             70.16              98.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             13.32              11.49 
[1] "1.7 - 70.2 (13.3)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      6   10
  12P GAIN WILD-TYPE   29  102
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                     102
D21V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4   12
  12P GAIN WILD-TYPE   48   83
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 48
  MALE                 12                 83
                    vv
clus                  M0  M1 M1A M1B M1C
  12P GAIN MUTATED    13   1   1   0   0
  12P GAIN WILD-TYPE 115   0   1   2   1
D21V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P GAIN MUTATED    4  0   2   2  0   2   1   1  3  0
  12P GAIN WILD-TYPE 73  2   4  10  1   2  10   3 13  2
D21V6, multiclass
D21V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P GAIN MUTATED             0       1        1        1        0         0
  12P GAIN WILD-TYPE           1      15        7       12       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED           0         0         3          2          3
  12P GAIN WILD-TYPE         8         4         5          3         13
                    vv
clus                 STAGE IIIC STAGE IV
  12P GAIN MUTATED            2        2
  12P GAIN WILD-TYPE         19        2
D21V8, multiclass

Clustering(22) Variable = 12q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  4
  12Q GAIN WILD-TYPE 37 40
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 77 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 40 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-DA-A3F5 TCGA-EE-A2A6 TCGA-ER-A19L TCGA-GN-A26A 
       70.16        22.55        17.56         8.94        12.99        12.16 

$`12Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        32.55        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       21.14        11.41         6.35        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.09        11.31        25.28        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D 
       84.72        10.09        16.21        15.39        14.70 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              8.94               1.02 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16              98.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            15.275             11.570 
[1] "8.9 - 70.2 (15.3)" "1.0 - 98.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    5
  12Q GAIN WILD-TYPE   33  107
                                                                                          clus
vv                                                                                         12Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         12Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     107
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    6
  12Q GAIN WILD-TYPE   51   89
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 51
  MALE                  6                 89
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q GAIN MUTATED     6   0   0   0   0
  12Q GAIN WILD-TYPE 122   1   2   2   1
D22V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q GAIN MUTATED    1  0   2   1  0   1   0   0  1  0
  12Q GAIN WILD-TYPE 76  2   4  11  1   3  11   4 15  2
D22V6, multiclass
D22V7, 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           1      16        7       13       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED           0         0         1          2          1
  12Q GAIN WILD-TYPE         8         4         7          3         15
                    vv
clus                 STAGE IIIC STAGE IV
  12Q GAIN MUTATED            1        0
  12Q GAIN WILD-TYPE         20        4
D22V8, multiclass

Clustering(23) Variable = 13q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    5  8
  13Q GAIN WILD-TYPE 34 36
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                 70 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 36 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EE-A29P TCGA-EE-A29R 
       16.47        13.32        36.69         7.00        12.03         8.84 
TCGA-EE-A2A5 TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A3PL TCGA-GN-A267 
        9.67        12.99        28.64        42.84         1.71        16.21 
TCGA-GN-A268 
       15.39 

$`13Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.47         8.12         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       25.28        23.90         8.94         3.52        11.11         4.18 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       78.44         6.58         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        12.16        14.70 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              1.71               1.02 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             42.84              98.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.32              11.49 
[1] "1.7 - 42.8 (13.3)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   15
  13Q GAIN WILD-TYPE   29   97
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      97
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8   13
  13Q GAIN WILD-TYPE   44   82
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                8                 44
  MALE                 13                 82
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q GAIN MUTATED    17   0   1   0   0
  13Q GAIN WILD-TYPE 111   1   1   2   1
D23V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q GAIN MUTATED    9  0   3   3  0   0   2   0  1  0
  13Q GAIN WILD-TYPE 68  2   3   9  1   4   9   4 15  2
D23V6, multiclass
D23V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q GAIN MUTATED             0       1        0        3        0         1
  13Q GAIN WILD-TYPE           1      15        8       10       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED           1         2         1          2          3
  13Q GAIN WILD-TYPE         7         2         7          3         13
                    vv
clus                 STAGE IIIC STAGE IV
  13Q GAIN MUTATED            3        1
  13Q GAIN WILD-TYPE         18        3
D23V8, multiclass

Clustering(24) Variable = 14q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  5
  14Q GAIN WILD-TYPE 37 39
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 5                 39 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A29L TCGA-ER-A19L TCGA-ER-A19M 
       22.55        13.68        36.69         1.08        12.99        28.64 
TCGA-GN-A26D 
       14.70 

$`14Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        39.19         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        3.52        11.11         4.18        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       10.09        16.21        15.39        12.16 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               1.02 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             36.69              98.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.70              11.49 
[1] "1.1 - 36.7 (14.7)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED"   "14Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" 
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    9
  14Q GAIN WILD-TYPE   32  103
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         14Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     103
D24V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      4    8
  14Q GAIN WILD-TYPE   48   87
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 48
  MALE                  8                 87
                    vv
clus                  M0  M1 M1A M1B M1C
  14Q GAIN MUTATED    10   0   0   0   0
  14Q GAIN WILD-TYPE 118   1   2   2   1
D24V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q GAIN MUTATED    7  0   0   0  0   1   2   0  1  0
  14Q GAIN WILD-TYPE 70  2   6  12  1   3   9   4 15  2
D24V6, multiclass
D24V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q GAIN MUTATED             0       1        1        1        2         0
  14Q GAIN WILD-TYPE           1      15        7       12       15         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED           0         2         0          0          2
  14Q GAIN WILD-TYPE         8         2         8          5         14
                    vv
clus                 STAGE IIIC STAGE IV
  14Q GAIN MUTATED            2        0
  14Q GAIN WILD-TYPE         19        4
D24V8, multiclass

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    5  9
  15Q GAIN WILD-TYPE 34 35
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                 69 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 9                 35 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1HW 
       32.55        22.55        21.14        13.32         5.39        35.80 
TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A29D TCGA-EE-A2A1 TCGA-ER-A19M 
       36.69        17.56        12.20        11.15        25.28        28.64 
TCGA-FR-A44A TCGA-GN-A264 
       72.16        31.33 

$`15Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        70.16        98.76        28.08        10.26         8.38 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        15.25        45.70        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        4.01         2.86        48.79        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       13.68         9.99        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 
        7.00        14.83        11.57         6.31         1.12         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       36.07         5.13        37.97        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
        8.09        11.31        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11         4.18        12.99        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        1.71         5.95         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        1.02        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.39               1.02 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.16              98.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            23.915             11.110 
[1] "5.4 - 72.2 (23.9)" "1.0 - 98.8 (11.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5   16
  15Q GAIN WILD-TYPE   30   96
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    16
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      96
D25V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   13
  15Q GAIN WILD-TYPE   44   82
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                 44
  MALE                 13                 82
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q GAIN MUTATED    20   0   0   0   0
  15Q GAIN WILD-TYPE 108   1   2   2   1
D25V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q GAIN MUTATED   11  0   0   4  0   2   1   0  2  0
  15Q GAIN WILD-TYPE 66  2   6   8  1   2  10   4 14  2
D25V6, multiclass
D25V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q GAIN MUTATED             1       3        1        2        2         1
  15Q GAIN WILD-TYPE           0      13        7       11       15         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED           0         1         1          0          4
  15Q GAIN WILD-TYPE         8         3         7          5         12
                    vv
clus                 STAGE IIIC STAGE IV
  15Q GAIN MUTATED            3        0
  15Q GAIN WILD-TYPE         18        4
D25V8, multiclass

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  5
  16P GAIN WILD-TYPE 38 39
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 77 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 39 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19M 
       70.16        13.32         8.84         9.67         3.52        28.64 

$`16P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        6.48         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11         4.18        12.99        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.52               1.02 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             70.16              98.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            11.495             12.160 
[1] "3.5 - 70.2 (11.5)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    7
  16P GAIN WILD-TYPE   30  105
                                                                                          clus
vv                                                                                         16P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     105
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    7
  16P GAIN WILD-TYPE   47   88
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 47
  MALE                  7                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  16P GAIN MUTATED    12   0   0   0   0
  16P GAIN WILD-TYPE 116   1   2   2   1
D26V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P GAIN MUTATED    8  0   1   3  0   0   0   0  0  0
  16P GAIN WILD-TYPE 69  2   5   9  1   4  11   4 16  2
D26V6, multiclass
D26V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P GAIN MUTATED             0       1        1        3        1         1
  16P GAIN WILD-TYPE           1      15        7       10       16         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED           0         1         2          1          0
  16P GAIN WILD-TYPE         8         3         6          4         16
                    vv
clus                 STAGE IIIC STAGE IV
  16P GAIN MUTATED            1        0
  16P GAIN WILD-TYPE         20        4
D26V8, multiclass

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  4
  16Q GAIN WILD-TYPE 38 40
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 78 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 40 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A29R TCGA-ER-A19D TCGA-ER-A19M 
       70.16        13.32         8.84         3.52        28.64 

$`16Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        4.41         1.08         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 
        8.94        11.11         4.18        12.99        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        16.21        15.39        12.16        14.70 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.52               1.02 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             70.16              98.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            13.320             12.095 
[1] "3.5 - 70.2 (13.3)" "1.0 - 98.8 (12.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    6
  16Q GAIN WILD-TYPE   31  106
                                                                                          clus
vv                                                                                         16Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                     106
D27V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    6
  16Q GAIN WILD-TYPE   48   89
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                 48
  MALE                  6                 89
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q GAIN MUTATED    10   0   0   0   0
  16Q GAIN WILD-TYPE 118   1   2   2   1
D27V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q GAIN MUTATED    5  0   1   4  0   0   0   0  0  0
  16Q GAIN WILD-TYPE 72  2   5   8  1   4  11   4 16  2
D27V6, multiclass
D27V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q GAIN MUTATED             0       1        0        2        0         1
  16Q GAIN WILD-TYPE           1      15        8       11       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED           0         1         2          1          1
  16Q GAIN WILD-TYPE         8         3         6          4         15
                    vv
clus                 STAGE IIIC STAGE IV
  16Q GAIN MUTATED            1        0
  16Q GAIN WILD-TYPE         20        4
D27V8, multiclass

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    7  3
  17P GAIN WILD-TYPE 32 41
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                10                 73 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 41 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-EE-A20F TCGA-EE-A29N 
       16.47        13.32         5.39        36.69         5.13         9.47 
TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-GN-A26D 
       12.03         8.94         1.71        14.70 

$`17P GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       24.00         9.30         4.01         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       51.12        10.03        39.19        13.68         9.99        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29Q 
       37.97        11.15        38.63         4.41         1.08         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       23.90         9.67         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       28.64        42.84        78.44         6.58         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A 
       12.16 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.71               1.02 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.69              98.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             10.75              12.20 
[1] "1.7 - 36.7 (10.8)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
[1] "hr=" "1.3"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    8
  17P GAIN WILD-TYPE   30  104
                                                                                          clus
vv                                                                                         17P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     104
D28V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6    7
  17P GAIN WILD-TYPE   46   88
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                6                 46
  MALE                  7                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  17P GAIN MUTATED    10   0   1   0   0
  17P GAIN WILD-TYPE 118   1   1   2   1
D28V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P GAIN MUTATED    8  0   0   1  0   1   1   0  1  0
  17P GAIN WILD-TYPE 69  2   6  11  1   3  10   4 15  2
D28V6, multiclass
D28V7, 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           1      16        7       13       16         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED           0         3         1          0          2
  17P GAIN WILD-TYPE         8         1         7          5         14
                    vv
clus                 STAGE IIIC STAGE IV
  17P GAIN MUTATED            1        1
  17P GAIN WILD-TYPE         20        3
D28V8, multiclass

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    8  8
  17Q GAIN WILD-TYPE 31 36
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 67 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 36 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JD TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-DA-A1IC 
       16.47        11.41        13.32         5.39        36.69         6.64 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A6 
        1.12         4.27         5.13         9.47        12.03         8.94 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-GN-A268 TCGA-GN-A26D 
        1.71         5.95        15.39        14.70 

$`17Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
        8.38        21.14         6.35        15.25        45.70        24.00 
TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        9.30         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB 
       10.03        39.19        13.68         9.99        25.15        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       19.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       12.20        36.07        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        1.08         8.12         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F 
       11.31        25.28        23.90         9.67         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.35        24.85        31.33        84.72        10.09        16.21 
TCGA-GN-A26A 
       12.16 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.12               1.02 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             36.69              98.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             9.205             13.680 
[1] "1.1 - 36.7 (9.2)"  "1.0 - 98.8 (13.7)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "1.7"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5   16
  17Q GAIN WILD-TYPE   30   96
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    16
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      96
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      9   12
  17Q GAIN WILD-TYPE   43   83
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                9                 43
  MALE                 12                 83
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q GAIN MUTATED    18   0   1   0   0
  17Q GAIN WILD-TYPE 110   1   1   2   1
D29V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q GAIN MUTATED   12  0   0   2  0   2   1   1  2  0
  17Q GAIN WILD-TYPE 65  2   6  10  1   2  10   3 14  2
D29V6, multiclass
D29V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q GAIN MUTATED             0       0        1        1        3         1
  17Q GAIN WILD-TYPE           1      16        7       12       14         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED           1         3         1          0          3
  17Q GAIN WILD-TYPE         7         1         7          5         13
                    vv
clus                 STAGE IIIC STAGE IV
  17Q GAIN MUTATED            3        1
  17Q GAIN WILD-TYPE         18        3
D29V8, multiclass

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  8
  18P GAIN WILD-TYPE 34 36
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                13                 70 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                 36 
$`18P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-DA-A1I0 TCGA-DA-A1I1 
       32.55        22.55        45.70        13.32        10.03        39.19 
TCGA-EE-A181 TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P TCGA-GN-A267 TCGA-GN-A26A 
        1.12        38.63         1.08        12.03        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`18P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       16.47        70.16        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MO 
       21.14        11.41         6.35        15.25        24.00         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
        5.39         4.01         2.86        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       19.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41         9.47         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR 
       78.44         6.58         1.71         5.95        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       31.33        84.72        10.09        15.39 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.08               1.02 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             45.70              98.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.70              11.36 
[1] "1.1 - 45.7 (14.7)" "1.0 - 98.8 (11.4)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" 
[1] "hr=" "1"  
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5   14
  18P GAIN WILD-TYPE   30   98
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    14
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      98
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      9   10
  18P GAIN WILD-TYPE   43   85
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                9                 43
  MALE                 10                 85
                    vv
clus                  M0  M1 M1A M1B M1C
  18P GAIN MUTATED    16   0   1   0   0
  18P GAIN WILD-TYPE 112   1   1   2   1
D30V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P GAIN MUTATED    9  0   3   2  0   1   0   0  3  0
  18P GAIN WILD-TYPE 68  2   3  10  1   3  11   4 13  2
D30V6, multiclass
D30V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P GAIN MUTATED             1       3        0        0        1         0
  18P GAIN WILD-TYPE           0      13        8       13       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED           0         4         1          3          2
  18P GAIN WILD-TYPE         8         0         7          2         14
                    vv
clus                 STAGE IIIC STAGE IV
  18P GAIN MUTATED            3        0
  18P GAIN WILD-TYPE         18        4
D30V8, multiclass

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    3  4
  18Q GAIN WILD-TYPE 36 40
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                 76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 40 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EE-A29L TCGA-GN-A267 TCGA-GN-A26A 
       32.55        45.70        39.19         1.08        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`18Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR 
       78.44         6.58         1.71         5.95        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       31.33        84.72        10.09        15.39 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               1.02 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             45.70              98.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             16.21              11.49 
[1] "1.1 - 45.7 (16.2)" "1.0 - 98.8 (11.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" 
[1] "hr=" "1.3"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    6
  18Q GAIN WILD-TYPE   31  106
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                     106
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    6
  18Q GAIN WILD-TYPE   48   89
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 48
  MALE                  6                 89
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q GAIN MUTATED     8   0   0   0   0
  18Q GAIN WILD-TYPE 120   1   2   2   1
D31V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q GAIN MUTATED    5  0   2   0  0   0   0   0  2  0
  18Q GAIN WILD-TYPE 72  2   4  12  1   4  11   4 14  2
D31V6, multiclass
D31V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q GAIN MUTATED             1       1        0        0        0         0
  18Q GAIN WILD-TYPE           0      15        8       13       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED           0         3         0          2          0
  18Q GAIN WILD-TYPE         8         1         8          3         16
                    vv
clus                 STAGE IIIC STAGE IV
  18Q GAIN MUTATED            2        0
  18Q GAIN WILD-TYPE         19        4
D31V8, multiclass

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    1  2
  19P GAIN WILD-TYPE 38 42
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 80 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 42 
$`19P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A29L TCGA-EE-A29R 
       32.55         1.08         8.84 

$`19P GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       38.63         4.41         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        8.94         3.52        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       42.84        78.44         6.58         1.71         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.08               1.02 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             32.55              98.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              8.84              12.18 
[1] "1.1 - 32.5 (8.8)"  "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    7
  19P GAIN WILD-TYPE   35  105
                                                                                          clus
vv                                                                                         19P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 35
  REGIONAL LYMPH NODE                                                                                     105
D32V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    4
  19P GAIN WILD-TYPE   49   91
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                 49
  MALE                  4                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  19P GAIN MUTATED     7   0   0   0   0
  19P GAIN WILD-TYPE 121   1   2   2   1
D32V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P GAIN MUTATED    5  0   0   1  0   0   0   0  1  0
  19P GAIN WILD-TYPE 72  2   6  11  1   4  11   4 15  2
D32V6, multiclass
D32V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P GAIN MUTATED             1       2        0        1        0         1
  19P GAIN WILD-TYPE           0      14        8       12       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED           0         0         0          0          0
  19P GAIN WILD-TYPE         8         4         8          5         16
                    vv
clus                 STAGE IIIC STAGE IV
  19P GAIN MUTATED            2        0
  19P GAIN WILD-TYPE         19        4
D32V8, multiclass

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  4
  19Q GAIN WILD-TYPE 36 40
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 40 
$`19Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A3CE TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29T 
       16.47        32.55        13.32         1.08         8.84         6.48 
TCGA-ER-A3ET 
        6.58 

$`19Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       70.16        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        45.70        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
        9.30         5.39         4.01         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       51.12        10.03        39.19        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         8.12         9.99         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL 
        4.18        12.99        28.64        42.84        78.44         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        1.02        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        15.39        12.16        14.70 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.08               1.02 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.55              98.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              8.84              12.18 
[1] "1.1 - 32.5 (8.8)"  "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19Q GAIN MUTATED"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2    9
  19Q GAIN WILD-TYPE   33  103
                                                                                          clus
vv                                                                                         19Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         19Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     103
D33V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7    4
  19Q GAIN WILD-TYPE   45   91
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                7                 45
  MALE                  4                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q GAIN MUTATED    11   0   0   0   0
  19Q GAIN WILD-TYPE 117   1   2   2   1
D33V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q GAIN MUTATED    5  0   1   2  0   0   0   0  2  1
  19Q GAIN WILD-TYPE 72  2   5  10  1   4  11   4 14  1
D33V6, multiclass
D33V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q GAIN MUTATED             1       1        0        1        0         1
  19Q GAIN WILD-TYPE           0      15        8       12       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED           1         0         1          1          0
  19Q GAIN WILD-TYPE         7         4         7          4         16
                    vv
clus                 STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3        0
  19Q GAIN WILD-TYPE         18        4
D33V8, multiclass

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    9 12
  20P GAIN WILD-TYPE 30 32
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                21                 62 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 32 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I0 
       16.47        32.55        22.55        13.32         5.39        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29R TCGA-EE-A2A1 
       13.68        36.69        17.56        36.07         8.84        25.28 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A3YN 
        9.67         8.94         4.18        12.99        28.64         5.95 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        12.16        14.70 

$`20P GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       70.16        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        15.25        45.70        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 
        4.01         2.86        48.79        35.80        51.12        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
        9.47        12.03         8.12         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 
       11.31        23.90         3.52        11.11        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        6.58         1.71        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02        15.35        24.85        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.18               1.02 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             36.69              98.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             13.68              11.36 
[1] "4.2 - 36.7 (13.7)" "1.0 - 98.8 (11.4)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20P GAIN MUTATED"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" 
[1] "hr=" "1"  
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12   31
  20P GAIN WILD-TYPE   23   81
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               12
  REGIONAL LYMPH NODE                                                                                    31
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 23
  REGIONAL LYMPH NODE                                                                                      81
D34V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     15   28
  20P GAIN WILD-TYPE   37   67
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               15                 37
  MALE                 28                 67
                    vv
clus                 M0 M1 M1A M1B M1C
  20P GAIN MUTATED   37  1   1   0   0
  20P GAIN WILD-TYPE 91  0   1   2   1
D34V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P GAIN MUTATED   23  0   3   3  0   2   3   1  4  1
  20P GAIN WILD-TYPE 54  2   3   9  1   2   8   3 12  1
D34V6, multiclass
D34V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20P GAIN MUTATED             1       5        5        4        4         2
  20P GAIN WILD-TYPE           0      11        3        9       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED           0         2         2          2          4
  20P GAIN WILD-TYPE         8         2         6          3         12
                    vv
clus                 STAGE IIIC STAGE IV
  20P GAIN MUTATED            7        1
  20P GAIN WILD-TYPE         14        3
D34V8, multiclass

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   14 13
  20Q GAIN WILD-TYPE 25 31
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                27                 56 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 31 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1HV 
       16.47        32.55        22.55        13.32         5.39        48.79 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29E 
       10.03        13.68        36.69        17.56        36.07        38.63 
TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 
        1.08        12.03         8.84        25.28         9.67         8.94 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
        4.18        12.99        28.64         1.71         5.95        72.16 
TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        12.16        14.70 

$`20Q GAIN WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       70.16        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        15.25        45.70        24.00         9.30 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 
        4.01         2.86        35.80        51.12        39.19         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
       25.15        22.36         6.64        19.36         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         6.31         1.12        12.20         4.27         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S 
       37.97        11.15         4.41         9.47         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F 
        6.48         8.09        11.31        23.90         3.52        11.11 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
       42.84        78.44         6.58         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02        15.35        24.85        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.08               1.02 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             72.16              98.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             13.68              11.23 
[1] "1.1 - 72.2 (13.7)" "1.0 - 98.8 (11.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     14   39
  20Q GAIN WILD-TYPE   21   73
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               14
  REGIONAL LYMPH NODE                                                                                    39
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 21
  REGIONAL LYMPH NODE                                                                                      73
D35V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     18   35
  20Q GAIN WILD-TYPE   34   60
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               18                 34
  MALE                 35                 60
                    vv
clus                 M0 M1 M1A M1B M1C
  20Q GAIN MUTATED   43  1   2   1   0
  20Q GAIN WILD-TYPE 85  0   0   1   1
D35V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20Q GAIN MUTATED   27  0   3   4  0   2   4   1  6  1
  20Q GAIN WILD-TYPE 50  2   3   8  1   2   7   3 10  1
D35V6, multiclass
D35V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  20Q GAIN MUTATED             1       5        5        4        6         2
  20Q GAIN WILD-TYPE           0      11        3        9       11         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED           0         3         2          2          6
  20Q GAIN WILD-TYPE         8         1         6          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  20Q GAIN MUTATED            8        2
  20Q GAIN WILD-TYPE         13        2
D35V8, multiclass

Clustering(36) Variable = 21q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    6  5
  21Q GAIN WILD-TYPE 33 39
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                 72 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 5                 39 
$`21Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        5.39         1.08         8.84        11.31        25.28         9.67 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN TCGA-GN-A26D 
        3.52        12.99         1.71         5.95        14.70 

$`21Q GAIN WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        13.32        24.00         9.30         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       38.63         4.41         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        6.48         8.09        23.90         8.94        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A1ZR 
       28.64        42.84        78.44         6.58        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.09        16.21        15.39        12.16 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.08               1.02 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.28              98.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              8.84              13.50 
[1] "1.1 - 25.3 (8.8)"  "1.0 - 98.8 (13.5)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"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-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"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-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"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-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
[1] "hr=" "1.9"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      6   11
  21Q GAIN WILD-TYPE   29  101
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                     101
D36V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8    9
  21Q GAIN WILD-TYPE   44   86
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                 44
  MALE                  9                 86
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q GAIN MUTATED    14   0   1   0   0
  21Q GAIN WILD-TYPE 114   1   1   2   1
D36V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q GAIN MUTATED   12  0   0   1  0   2   0   0  1  0
  21Q GAIN WILD-TYPE 65  2   6  11  1   2  11   4 15  2
D36V6, multiclass
D36V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q GAIN MUTATED             0       1        0        4        1         3
  21Q GAIN WILD-TYPE           1      15        8        9       16         4
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED           0         2         0          1          1
  21Q GAIN WILD-TYPE         8         2         8          4         15
                    vv
clus                 STAGE IIIC STAGE IV
  21Q GAIN MUTATED            2        1
  21Q GAIN WILD-TYPE         19        3
D36V8, multiclass

Clustering(37) Variable = 22q gain mutation analysis
D37V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   12 11
  22Q GAIN WILD-TYPE 27 33
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                 60 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                 33 
$`22Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HV TCGA-DA-A1I0 
       16.47        22.55         9.30         5.39        48.79        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F5 TCGA-EE-A29L 
       39.19        36.69        25.15        22.36        17.56         1.08 
TCGA-EE-A29N TCGA-EE-A29R TCGA-ER-A19M TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
        9.47         8.84        28.64         6.58         5.95        72.16 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.21        12.16        14.70 

$`22Q GAIN WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        70.16        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       21.14        11.41         6.35        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I2 
       24.00         4.01         2.86        35.80        51.12        13.68 
TCGA-DA-A1I4 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X 
        9.99         6.64        19.36         7.00        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q 
       37.97        11.15        38.63         4.41        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        9.67         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
       42.84        78.44         1.71         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
        6.41         1.02        15.35        24.85        10.09        15.39 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.08               1.02 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             84.72              98.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             16.47              11.36 
[1] "1.1 - 84.7 (16.5)" "1.0 - 98.8 (11.4)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
[1] "hr=" "1.5"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   24
  22Q GAIN WILD-TYPE   22   88
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               13
  REGIONAL LYMPH NODE                                                                                    24
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 22
  REGIONAL LYMPH NODE                                                                                      88
D37V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     14   23
  22Q GAIN WILD-TYPE   38   72
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               14                 38
  MALE                 23                 72
                    vv
clus                 M0 M1 M1A M1B M1C
  22Q GAIN MUTATED   31  0   1   1   0
  22Q GAIN WILD-TYPE 97  1   1   1   1
D37V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q GAIN MUTATED   14  0   4   1  0   3   3   2  7  0
  22Q GAIN WILD-TYPE 63  2   2  11  1   1   8   2  9  2
D37V6, multiclass
D37V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q GAIN MUTATED             0       2        1        2        4         2
  22Q GAIN WILD-TYPE           1      14        7       11       13         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED           0         2         2          5          4
  22Q GAIN WILD-TYPE         8         2         6          0         12
                    vv
clus                 STAGE IIIC STAGE IV
  22Q GAIN MUTATED            8        0
  22Q GAIN WILD-TYPE         13        4
D37V8, multiclass

Clustering(38) Variable = 1p loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    4  2
  1P LOSS WILD-TYPE 35 42
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                77 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                42 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-DA-A1I7 TCGA-EE-A29R TCGA-ER-A19L TCGA-GN-A26D 
       22.55        45.70        36.69         8.84        12.99        14.70 

$`1P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
        1.08         9.47        12.03         8.12         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39        12.16 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             8.84              1.02 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            45.70             98.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           18.625            11.570 
[1] "8.8 - 45.7 (18.6)" "1.0 - 98.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "2.2"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      4    8
  1P LOSS WILD-TYPE   31  104
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    104
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6    6
  1P LOSS WILD-TYPE   46   89
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6                46
  MALE                 6                89
                   vv
clus                 M0  M1 M1A M1B M1C
  1P LOSS MUTATED     9   0   0   0   0
  1P LOSS WILD-TYPE 119   1   2   2   1
D38V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P LOSS MUTATED    6  0   0   1  0   1   2   0  0  0
  1P LOSS WILD-TYPE 71  2   6  11  1   3   9   4 16  2
D38V6, multiclass
D38V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P LOSS MUTATED             0       0        0        0        4         0
  1P LOSS WILD-TYPE           1      16        8       13       13         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P LOSS MUTATED           0         2         1          0          2
  1P LOSS WILD-TYPE         8         2         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  1P LOSS MUTATED            1        0
  1P LOSS WILD-TYPE         20        4
D38V8, multiclass

Clustering(39) Variable = 1q loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  2
  1Q LOSS WILD-TYPE 37 42
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                79 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                42 
$`1Q LOSS MUTATED`
TCGA-D3-A3CC TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A29X 
       45.70        36.69        25.15         8.09 

$`1Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        9.99        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        6.48        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR 
       78.44         6.58         1.71         5.95        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        10.09        16.21        15.39        12.16 
TCGA-GN-A26D 
       14.70 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.09              1.02 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            45.70             98.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            30.92             12.03 
[1] "8.1 - 45.7 (30.9)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED"   "1Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    1
  1Q LOSS WILD-TYPE   32  111
                                                                                          clus
vv                                                                                         1Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         1Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    111
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    1
  1Q LOSS WILD-TYPE   49   94
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                49
  MALE                 1                94
                   vv
clus                 M0  M1 M1A M1B M1C
  1Q LOSS MUTATED     4   0   0   0   0
  1Q LOSS WILD-TYPE 124   1   2   2   1
D39V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q LOSS MUTATED    2  0   0   0  0   0   1   0  1  0
  1Q LOSS WILD-TYPE 75  2   6  12  1   4  10   4 15  2
D39V6, multiclass
D39V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q LOSS MUTATED             0       0        0        1        0         0
  1Q LOSS WILD-TYPE           1      16        8       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q LOSS MUTATED           0         1         0          0          1
  1Q LOSS WILD-TYPE         8         3         8          5         15
                   vv
clus                STAGE IIIC STAGE IV
  1Q LOSS MUTATED            1        0
  1Q LOSS WILD-TYPE         20        4
D39V8, multiclass

Clustering(40) Variable = 2p loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    4  4
  2P LOSS WILD-TYPE 35 40
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8                75 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                40 
$`2P LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z3 TCGA-DA-A1I2 TCGA-EE-A20B TCGA-EE-A20F 
       15.25        24.00         2.86        13.68        36.07         5.13 
TCGA-GN-A264 TCGA-GN-A26D 
       31.33        14.70 

$`2P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC 
       10.26         8.38        21.14        11.41         6.35        45.70 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW 
       13.32         9.30         5.39         4.01        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       51.12        10.03        39.19         9.99        36.69        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C 
       11.57         6.31         1.12        12.20         4.27        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02        15.35        24.85        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       16.21        15.39        12.16 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.86              1.02 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            36.07             98.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.975            11.570 
[1] "2.9 - 36.1 (15.0)" "1.0 - 98.8 (11.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   12
  2P LOSS WILD-TYPE   33  100
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    100
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    9
  2P LOSS WILD-TYPE   47   86
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               5                47
  MALE                 9                86
                   vv
clus                 M0  M1 M1A M1B M1C
  2P LOSS MUTATED    11   0   0   0   0
  2P LOSS WILD-TYPE 117   1   2   2   1
D40V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P LOSS MUTATED    9  0   0   1  0   0   1   0  1  0
  2P LOSS WILD-TYPE 68  2   6  11  1   4  10   4 15  2
D40V6, multiclass
D40V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2P LOSS MUTATED             0       0        0        2        5         0
  2P LOSS WILD-TYPE           1      16        8       11       12         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P LOSS MUTATED           1         1         0          0          1
  2P LOSS WILD-TYPE         7         3         8          5         15
                   vv
clus                STAGE IIIC STAGE IV
  2P LOSS MUTATED            2        0
  2P LOSS WILD-TYPE         19        4
D40V8, multiclass

Clustering(41) Variable = 2q loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    3  3
  2Q LOSS WILD-TYPE 36 41
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6                77 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                41 
$`2Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-GN-A26D 
       15.25        24.00        36.07         5.13        11.15        14.70 

$`2Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC 
       10.26         8.38        21.14        11.41         6.35        45.70 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       13.32         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        4.27        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
       12.03         8.12         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       11.31        25.28        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       84.72        10.09        16.21        15.39        12.16 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5.13              1.02 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            36.07             98.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           14.975            12.030 
[1] "5.1 - 36.1 (15.0)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "hr=" "1.2"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   11
  2Q LOSS WILD-TYPE   33  101
                                                                                          clus
vv                                                                                         2Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   11
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    101
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    7
  2Q LOSS WILD-TYPE   46   88
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               6                46
  MALE                 7                88
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q LOSS MUTATED    10   0   0   1   0
  2Q LOSS WILD-TYPE 118   1   2   1   1
D41V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q LOSS MUTATED    9  0   0   1  0   0   0   0  2  0
  2Q LOSS WILD-TYPE 68  2   6  11  1   4  11   4 14  2
D41V6, multiclass
D41V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  2Q LOSS MUTATED             0       0        0        2        5         0
  2Q LOSS WILD-TYPE           1      16        8       11       12         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q LOSS MUTATED           1         1         0          0          0
  2Q LOSS WILD-TYPE         7         3         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2        0
  2Q LOSS WILD-TYPE         19        4
D41V8, multiclass

Clustering(42) Variable = 3p loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    2  4
  3P LOSS WILD-TYPE 37 40
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                77 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                40 
$`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-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB 
       51.12        10.03        39.19         9.99        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
       37.97        11.15        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X 
       12.03         8.12         8.84         9.99         6.48         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       11.31        25.28        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 
       10.78         6.41         1.02        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.68              1.02 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            36.69             98.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            28.70             11.41 
[1] "13.7 - 36.7 (28.7)" "1.0 - 98.8 (11.4)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3P LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3P LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3P LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    5
  3P LOSS WILD-TYPE   30  107
                                                                                          clus
vv                                                                                         3P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         3P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    107
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    6
  3P LOSS WILD-TYPE   48   89
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               4                48
  MALE                 6                89
                   vv
clus                 M0  M1 M1A M1B M1C
  3P LOSS MUTATED     8   0   0   0   0
  3P LOSS WILD-TYPE 120   1   2   2   1
D42V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P LOSS MUTATED    4  0   0   1  0   0   2   1  0  0
  3P LOSS WILD-TYPE 73  2   6  11  1   4   9   3 16  2
D42V6, multiclass
D42V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P LOSS MUTATED             1       2        0        1        0         0
  3P LOSS WILD-TYPE           0      14        8       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P LOSS MUTATED           0         0         1          0          2
  3P LOSS WILD-TYPE         8         4         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  3P LOSS MUTATED            1        0
  3P LOSS WILD-TYPE         20        4
D42V8, multiclass

Clustering(43) Variable = 3q loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    3  6
  3Q LOSS WILD-TYPE 36 38
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                74 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                6                38 
$`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 TCGA-GN-A264 TCGA-GN-A268 
       24.85        31.33        15.39 

$`3Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB 
       51.12        10.03        39.19         9.99        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        6.41         1.02        15.35        84.72        10.09        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.41              1.02 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            36.69             98.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            24.85             11.36 
[1] "4.4 - 36.7 (24.9)" "1.0 - 98.8 (11.4)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3Q LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3Q LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"3Q LOSS WILD-TYPE" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    8
  3Q LOSS WILD-TYPE   31  104
                                                                                          clus
vv                                                                                         3Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         3Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    104
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    6
  3Q LOSS WILD-TYPE   46   89
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6                46
  MALE                 6                89
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q LOSS MUTATED    10   0   0   0   0
  3Q LOSS WILD-TYPE 118   1   2   2   1
D43V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q LOSS MUTATED    6  0   0   1  0   0   2   1  0  0
  3Q LOSS WILD-TYPE 71  2   6  11  1   4   9   3 16  2
D43V6, multiclass
D43V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q LOSS MUTATED             1       1        2        1        0         0
  3Q LOSS WILD-TYPE           0      15        6       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q LOSS MUTATED           1         0         1          0          2
  3Q LOSS WILD-TYPE         7         4         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  3Q LOSS MUTATED            1        0
  3Q LOSS WILD-TYPE         20        4
D43V8, multiclass

Clustering(44) Variable = 4p loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  5
  4P LOSS WILD-TYPE 36 39
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                75 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                39 
$`4P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EE-A29C 
       16.47        10.26        45.70         2.86        35.80        37.97 
TCGA-ER-A19D TCGA-GN-A266 
        3.52        10.09 

$`4P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 
       32.55        70.16        98.76        28.08        22.55         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30         5.39         4.01        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
       25.28        23.90         9.67         8.94        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        1.02        15.35        24.85        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             2.86              1.02 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            45.70             98.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           13.365            12.160 
[1] "2.9 - 45.7 (13.4)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    9
  4P LOSS WILD-TYPE   29  103
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                    103
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    7
  4P LOSS WILD-TYPE   44   88
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               8                44
  MALE                 7                88
                   vv
clus                 M0  M1 M1A M1B M1C
  4P LOSS MUTATED    12   0   0   1   0
  4P LOSS WILD-TYPE 116   1   2   1   1
D44V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P LOSS MUTATED    8  0   0   2  0   1   0   0  2  0
  4P LOSS WILD-TYPE 69  2   6  10  1   3  11   4 14  2
D44V6, multiclass
D44V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             0       1        0        2        2         0
  4P LOSS WILD-TYPE           1      15        8       11       15         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P LOSS MUTATED           1         2         0          1          2
  4P LOSS WILD-TYPE         7         2         8          4         14
                   vv
clus                STAGE IIIC STAGE IV
  4P LOSS MUTATED            1        0
  4P LOSS WILD-TYPE         20        4
D44V8, multiclass

Clustering(45) Variable = 4q loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  6
  4Q LOSS WILD-TYPE 36 38
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                9                74 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                38 
$`4Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q8 TCGA-D3-A3CC TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-EE-A181 
       16.47        28.08        45.70         2.86        35.80         1.12 
TCGA-EE-A29C TCGA-ER-A19D TCGA-GN-A266 
       37.97         3.52        10.09 

$`4Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        70.16        98.76        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        15.25        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30         5.39         4.01        48.79        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D 
        6.31        12.20         4.27        36.07         5.13        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       23.90         9.67         8.94        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       28.64        42.84        78.44         6.58         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.35        24.85        31.33        84.72        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.12              1.02 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            45.70             98.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           16.470            12.095 
[1] "1.1 - 45.7 (16.5)" "1.0 - 98.8 (12.1)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "4Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "4Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "4Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6   10
  4Q LOSS WILD-TYPE   29  102
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                    102
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    7
  4Q LOSS WILD-TYPE   43   88
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               9                43
  MALE                 7                88
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q LOSS MUTATED    12   0   0   2   0
  4Q LOSS WILD-TYPE 116   1   2   0   1
D45V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q LOSS MUTATED    8  0   0   2  0   1   0   0  3  0
  4Q LOSS WILD-TYPE 69  2   6  10  1   3  11   4 13  2
D45V6, multiclass
D45V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       1        0        2        3         0
  4Q LOSS WILD-TYPE           1      15        8       11       14         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED           0         2         0          1          2
  4Q LOSS WILD-TYPE         8         2         8          4         14
                   vv
clus                STAGE IIIC STAGE IV
  4Q LOSS MUTATED            1        1
  4Q LOSS WILD-TYPE         20        3
D45V8, multiclass

Clustering(46) Variable = 5p loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    5  5
  5P LOSS WILD-TYPE 34 39
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               10                73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                39 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-DA-A1HV TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E 
       16.47        48.79        11.57         4.27        37.97        38.63 
TCGA-EE-A2A2 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
       23.90        24.85        10.09        15.39 

$`5P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       35.80        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B 
       17.56        14.83         6.31         1.12        12.20        36.07 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        5.13        11.15         4.41         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       25.28         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A 
        1.02        15.35        31.33        84.72        16.21        12.16 
TCGA-GN-A26D 
       14.70 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             4.27              1.02 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            48.79             98.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           20.185            11.410 
[1] "4.3 - 48.8 (20.2)" "1.0 - 98.8 (11.4)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   14
  5P LOSS WILD-TYPE   31   98
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   14
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                     98
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      8   10
  5P LOSS WILD-TYPE   44   85
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               8                44
  MALE                10                85
                   vv
clus                 M0  M1 M1A M1B M1C
  5P LOSS MUTATED    15   0   0   0   0
  5P LOSS WILD-TYPE 113   1   2   2   1
D46V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P LOSS MUTATED    7  0   0   2  0   1   2   1  2  0
  5P LOSS WILD-TYPE 70  2   6  10  1   3   9   3 14  2
D46V6, multiclass
D46V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       2        2        1        1         0
  5P LOSS WILD-TYPE           1      14        6       12       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P LOSS MUTATED           1         0         1          1          3
  5P LOSS WILD-TYPE         7         4         7          4         13
                   vv
clus                STAGE IIIC STAGE IV
  5P LOSS MUTATED            3        0
  5P LOSS WILD-TYPE         18        4
D46V8, multiclass

Clustering(47) Variable = 5q loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    7 10
  5Q LOSS WILD-TYPE 32 34
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               17                66 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               10                34 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HV 
       28.08         6.35        15.25        24.00         4.01        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C 
       35.80        10.03        36.69        11.57         4.27        37.97 
TCGA-EE-A29E TCGA-EE-A2A2 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
       38.63        23.90        24.85        10.09        15.39 

$`5Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO 
        8.38        21.14        11.41        45.70        13.32         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
        5.39         2.86        51.12        39.19        13.68         9.99 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
       14.83         6.31         1.12        12.20        36.07         5.13 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15         4.41         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.84         9.99         6.48         8.09        11.31        25.28 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        9.67         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       28.64        42.84        78.44         6.58         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       15.35        31.33        84.72        16.21        12.16        14.70 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             4.01              1.02 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            48.79             98.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.90             11.36 
[1] "4.0 - 48.8 (23.9)" "1.0 - 98.8 (11.4)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "5Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "5Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "5Q LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7   24
  5Q LOSS WILD-TYPE   28   88
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   24
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                28
  REGIONAL LYMPH NODE                                                                                     88
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     12   19
  5Q LOSS WILD-TYPE   40   76
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              12                40
  MALE                19                76
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q LOSS MUTATED    25   0   1   1   0
  5Q LOSS WILD-TYPE 103   1   1   1   1
D47V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q LOSS MUTATED   12  0   0   3  0   1   4   1  5  1
  5Q LOSS WILD-TYPE 65  2   6   9  1   3   7   3 11  1
D47V6, multiclass
D47V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             0       4        2        2        2         1
  5Q LOSS WILD-TYPE           1      12        6       11       15         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED           1         0         1          1          5
  5Q LOSS WILD-TYPE         7         4         7          4         11
                   vv
clus                STAGE IIIC STAGE IV
  5Q LOSS MUTATED            6        1
  5Q LOSS WILD-TYPE         15        3
D47V8, multiclass

Clustering(48) Variable = 6p loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    2  6
  6P LOSS WILD-TYPE 37 38
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                75 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                38 
$`6P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29D TCGA-EE-A29Q 
       22.55        10.26        51.12        25.15        11.15         8.12 
TCGA-EE-A29X TCGA-EE-A2A0 
        8.09        11.31 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 
       16.47        32.55        70.16        98.76        28.08         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       21.14        11.41         6.35        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        10.03        39.19        13.68         9.99        36.69 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 
       12.03         8.84         9.99         6.48        25.28        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        9.67         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       28.64        42.84        78.44         6.58         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       15.35        24.85        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.09              1.02 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            51.12             98.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            11.23             12.20 
[1] "8.1 - 51.1 (11.2)" "1.0 - 98.8 (12.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6P LOSS MUTATED"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    8
  6P LOSS WILD-TYPE   32  104
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    104
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    6
  6P LOSS WILD-TYPE   47   89
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               5                47
  MALE                 6                89
                   vv
clus                 M0  M1 M1A M1B M1C
  6P LOSS MUTATED    11   0   0   0   0
  6P LOSS WILD-TYPE 117   1   2   2   1
D48V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P LOSS MUTATED    7  0   0   1  0   1   0   0  2  0
  6P LOSS WILD-TYPE 70  2   6  11  1   3  11   4 14  2
D48V6, multiclass
D48V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             0       1        0        2        1         1
  6P LOSS WILD-TYPE           1      15        8       11       16         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P LOSS MUTATED           2         0         0          0          1
  6P LOSS WILD-TYPE         6         4         8          5         15
                   vv
clus                STAGE IIIC STAGE IV
  6P LOSS MUTATED            3        0
  6P LOSS WILD-TYPE         18        4
D48V8, multiclass

Clustering(49) Variable = 6q loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   16 19
  6Q LOSS WILD-TYPE 23 25
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               35                48 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19                25 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3C6 TCGA-D9-A3Z3 
       16.47        32.55        22.55        10.26        15.25         2.86 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 
       48.79        51.12        39.19         9.99        36.69        25.15 
TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29C TCGA-EE-A29D 
        6.64        17.56         4.27        36.07        37.97        11.15 
TCGA-EE-A29H TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        4.41         8.12         9.99         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FW-A3R5 TCGA-GN-A268 TCGA-GN-A26A 
        1.71         8.81         1.02        15.39        12.16 

$`6Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       70.16        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
        6.35        45.70        13.32        24.00         9.30         5.39 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F2 
        4.01        35.80        10.03        13.68        22.36        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
        7.00        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        5.13        38.63         1.08         9.47        12.03         8.84 
TCGA-EE-A29T TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        6.48        12.99        28.64        42.84        78.44         6.58 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-GN-A261 
        5.95        72.16        53.82        10.78         6.41        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26D 
       24.85        31.33        84.72        10.09        16.21        14.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              1.08 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            51.12             98.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           11.150            13.155 
[1] "1.0 - 51.1 (11.2)" "1.1 - 98.8 (13.2)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     17   36
  6Q LOSS WILD-TYPE   18   76
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              17
  REGIONAL LYMPH NODE                                                                                   36
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                18
  REGIONAL LYMPH NODE                                                                                     76
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   32
  6Q LOSS WILD-TYPE   31   63
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              21                31
  MALE                32                63
                   vv
clus                M0 M1 M1A M1B M1C
  6Q LOSS MUTATED   46  1   1   1   1
  6Q LOSS WILD-TYPE 82  0   1   1   0
D49V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q LOSS MUTATED   26  0   2   4  1   1   4   3  8  1
  6Q LOSS WILD-TYPE 51  2   4   8  0   3   7   1  8  1
D49V6, multiclass
D49V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             1       2        3        7        5         2
  6Q LOSS WILD-TYPE           0      14        5        6       12         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q LOSS MUTATED           4         0         2          1          9
  6Q LOSS WILD-TYPE         4         4         6          4          7
                   vv
clus                STAGE IIIC STAGE IV
  6Q LOSS MUTATED            8        3
  6Q LOSS WILD-TYPE         13        1
D49V8, multiclass

Clustering(50) Variable = 8p loss mutation analysis
D50V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2  6
  8P LOSS WILD-TYPE 37 38
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                75 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                38 
$`8P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3C6 TCGA-D3-A3MO TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29H 
       16.47        15.25         9.30        12.20        37.97         4.41 
TCGA-EE-A2A5 TCGA-GN-A264 
        9.67        31.33 

$`8P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       24.00         5.39         4.01         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       51.12        10.03        39.19        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B 
       14.83        11.57         6.31         1.12         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        5.13        11.15        38.63         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         8.84         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       25.28        23.90         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        1.02        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             4.41              1.02 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.97             98.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           13.725            12.030 
[1] "4.4 - 38.0 (13.7)" "1.0 - 98.8 (12.0)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   14
  8P LOSS WILD-TYPE   33   98
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   14
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                     98
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5   11
  8P LOSS WILD-TYPE   47   84
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               5                47
  MALE                11                84
                   vv
clus                 M0  M1 M1A M1B M1C
  8P LOSS MUTATED    12   0   0   1   0
  8P LOSS WILD-TYPE 116   1   2   1   1
D50V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P LOSS MUTATED    9  0   0   0  0   1   0   1  2  0
  8P LOSS WILD-TYPE 68  2   6  12  1   3  11   3 14  2
D50V6, multiclass
D50V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             0       4        1        3        1         0
  8P LOSS WILD-TYPE           1      12        7       10       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P LOSS MUTATED           0         0         1          0          0
  8P LOSS WILD-TYPE         8         4         7          5         16
                   vv
clus                STAGE IIIC STAGE IV
  8P LOSS MUTATED            1        0
  8P LOSS WILD-TYPE         20        4
D50V8, multiclass

Clustering(51) Variable = 9p loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   18 30
  9P LOSS WILD-TYPE 21 14
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               48                35 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               30                14 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JK 
       16.47        32.55        70.16        28.08        10.26         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW 
       15.25        24.00         9.30         2.86        48.79        35.80 
TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IC 
       51.12        39.19        13.68         9.99        25.15         6.64 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
       11.57         1.12         4.27        36.07         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15        38.63         1.08         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F 
        9.99         8.09        11.31         9.67         3.52        11.11 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F0 
       12.99        28.64         1.71         5.95         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.78         6.41         1.02        15.39        12.16        14.70 

$`9P LOSS WILD-TYPE`
TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CC 
       98.76        22.55         8.38        21.14        11.41        45.70 
TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1I0 TCGA-DA-A1I7 TCGA-DA-A1IB 
       13.32         5.39         4.01        10.03        36.69        22.36 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A183 
       19.36         7.00        17.56        14.83         6.31        12.20 
TCGA-EE-A29H TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        4.41         8.84         6.48        25.28        23.90         8.94 
TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-GN-A261 
        4.18        42.84        78.44         6.58        72.16        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       24.85        31.33        84.72        10.09        16.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.02              4.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            70.16             98.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            11.23             15.35 
[1] "1.0 - 70.2 (11.2)" "4.0 - 98.8 (15.3)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
[1] "hr=" "1.9"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     25   57
  9P LOSS WILD-TYPE   10   55
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              25
  REGIONAL LYMPH NODE                                                                                   57
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     55
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   53
  9P LOSS WILD-TYPE   23   42
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29                23
  MALE                53                42
                   vv
clus                M0 M1 M1A M1B M1C
  9P LOSS MUTATED   72  0   1   2   1
  9P LOSS WILD-TYPE 56  1   1   0   0
D51V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9P LOSS MUTATED   46  0   4   8  1   0   4   4 10  0
  9P LOSS WILD-TYPE 31  2   2   4  0   4   7   0  6  2
D51V6, multiclass
D51V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             1       3        3        9       13         5
  9P LOSS WILD-TYPE           0      13        5        4        4         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P LOSS MUTATED           6         3         4          2          9
  9P LOSS WILD-TYPE         2         1         4          3          7
                   vv
clus                STAGE IIIC STAGE IV
  9P LOSS MUTATED           12        3
  9P LOSS WILD-TYPE          9        1
D51V8, multiclass

Clustering(52) Variable = 9q loss mutation analysis
D52V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   14 21
  9Q LOSS WILD-TYPE 25 23
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               35                48 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21                23 
$`9Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HW 
       16.47        32.55        28.08        15.25        48.79        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EE-A181 
       39.19        13.68         9.99        25.15         6.64         1.12 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       36.07         5.13        11.15         1.08         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19D 
        8.12         9.99         8.09        11.31        23.90         3.52 
TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4FC 
       11.11        28.64         1.71         8.81        53.82         6.41 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
        1.02        24.85        15.39        12.16        14.70 

$`9Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       70.16        98.76        22.55        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41         6.35        45.70        13.32        24.00         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I7 
        5.39         4.01         2.86        51.12        10.03        36.69 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
       22.36        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
        6.31        12.20         4.27        37.97        38.63         4.41 
TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J 
        8.84         6.48        25.28         9.67         8.94         4.18 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       12.99        42.84        78.44         6.58         5.95        72.16 
TCGA-FS-A4F9 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
       10.78        15.35        31.33        84.72        10.09        16.21 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1.02              2.86 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            53.82             98.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.030            12.595 
[1] "1.0 - 53.8 (12.0)" "2.9 - 98.8 (12.6)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
  "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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
[1] "hr=" "1.4"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     19   42
  9Q LOSS WILD-TYPE   16   70
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              19
  REGIONAL LYMPH NODE                                                                                   42
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                16
  REGIONAL LYMPH NODE                                                                                     70
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     27   34
  9Q LOSS WILD-TYPE   25   61
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              27                25
  MALE                34                61
                   vv
clus                M0 M1 M1A M1B M1C
  9Q LOSS MUTATED   51  0   1   2   1
  9Q LOSS WILD-TYPE 77  1   1   0   0
D52V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q LOSS MUTATED   33  0   4   4  1   1   4   3  6  0
  9Q LOSS WILD-TYPE 44  2   2   8  0   3   7   1 10  2
D52V6, multiclass
D52V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             1       1        2        6        9         3
  9Q LOSS WILD-TYPE           0      15        6        7        8         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q LOSS MUTATED           5         3         3          3          7
  9Q LOSS WILD-TYPE         3         1         5          2          9
                   vv
clus                STAGE IIIC STAGE IV
  9Q LOSS MUTATED            6        3
  9Q LOSS WILD-TYPE         15        1
D52V8, multiclass

Clustering(53) Variable = 10p loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   11 25
  10P LOSS WILD-TYPE 28 19
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                 47 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                25                 19 
$`10P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JK 
       16.47        32.55        70.16        98.76        28.08         6.35 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I1 
       13.32        24.00         9.30         2.86        35.80        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A17Z TCGA-EE-A185 
       13.68         9.99        36.69        25.15         6.31         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29X 
       36.07         5.13         4.41         1.08        12.03         8.09 
TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
        9.67         3.52        12.99         6.58         1.71         5.95 
TCGA-FS-A1ZR TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
        8.81        31.33        10.09        16.21        15.39        12.16 

$`10P LOSS WILD-TYPE`
TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3C6 
       22.55        10.26         8.38        21.14        11.41        15.25 
TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       45.70         5.39         4.01        48.79        51.12        10.03 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       11.57         1.12        12.20        37.97        11.15        38.63 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
        9.47         8.12         8.84         9.99         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M 
       25.28        23.90         8.94        11.11         4.18        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       42.84        78.44        72.16        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D 
        1.02        15.35        24.85        84.72        14.70 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               1.02 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.76              84.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.095             12.200 
[1] "1.1 - 98.8 (12.1)" "1.0 - 84.7 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20   44
  10P LOSS WILD-TYPE   15   68
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               20
  REGIONAL LYMPH NODE                                                                                    44
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 15
  REGIONAL LYMPH NODE                                                                                      68
D53V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     27   37
  10P LOSS WILD-TYPE   25   58
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               27                 25
  MALE                 37                 58
                    vv
clus                 M0 M1 M1A M1B M1C
  10P LOSS MUTATED   57  0   1   1   1
  10P LOSS WILD-TYPE 71  1   1   1   0
D53V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10P LOSS MUTATED   34  0   5   5  0   0   6   3  7  0
  10P LOSS WILD-TYPE 43  2   1   7  1   4   5   1  9  2
D53V6, multiclass
D53V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             1       6        4        6        9         2
  10P LOSS WILD-TYPE           0      10        4        7        8         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED           3         2         5          4          5
  10P LOSS WILD-TYPE         5         2         3          1         11
                    vv
clus                 STAGE IIIC STAGE IV
  10P LOSS MUTATED           10        3
  10P LOSS WILD-TYPE         11        1
D53V8, multiclass

Clustering(54) Variable = 10q loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   13 25
  10Q LOSS WILD-TYPE 26 19
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                38                 45 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                25                 19 
$`10Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D9-A3Z3 TCGA-DA-A1HW 
        6.35        15.25        13.32         9.30         2.86        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F8 
       39.19        13.68         9.99        36.69        25.15        14.83 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L 
        6.31         4.27        36.07         5.13         4.41         1.08 
TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19L 
       12.03         8.09         9.67         8.94         3.52        12.99 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 
        1.71         5.95         8.81        24.85        31.33        10.09 
TCGA-GN-A267 TCGA-GN-A26A 
       16.21        12.16 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A3CC TCGA-D3-A3CF 
       10.26         8.38        21.14        11.41        45.70        24.00 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1IB 
        5.39         4.01        48.79        51.12        10.03        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 
        6.64        19.36         7.00        17.56        11.57         1.12 
TCGA-EE-A183 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q 
       12.20        37.97        11.15        38.63         9.47         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        8.84         9.99         6.48        11.31        25.28        23.90 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11         4.18        28.64        42.84        78.44         6.58 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
       72.16        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       84.72        15.39        14.70 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.08               1.02 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.76              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            12.575             11.570 
[1] "1.1 - 98.8 (12.6)" "1.0 - 84.7 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     22   49
  10Q LOSS WILD-TYPE   13   63
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               22
  REGIONAL LYMPH NODE                                                                                    49
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 13
  REGIONAL LYMPH NODE                                                                                      63
D54V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     28   43
  10Q LOSS WILD-TYPE   24   52
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               28                 24
  MALE                 43                 52
                    vv
clus                 M0 M1 M1A M1B M1C
  10Q LOSS MUTATED   60  0   1   2   1
  10Q LOSS WILD-TYPE 68  1   1   0   0
D54V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10Q LOSS MUTATED   38  0   4   5  0   1   6   3  7  0
  10Q LOSS WILD-TYPE 39  2   2   7  1   3   5   1  9  2
D54V6, multiclass
D54V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             1       6        6        7        9         2
  10Q LOSS WILD-TYPE           0      10        2        6        8         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED           4         2         5          3          7
  10Q LOSS WILD-TYPE         4         2         3          2          9
                    vv
clus                 STAGE IIIC STAGE IV
  10Q LOSS MUTATED            8        3
  10Q LOSS WILD-TYPE         13        1
D54V8, multiclass

Clustering(55) Variable = 11p loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   10 16
  11P LOSS WILD-TYPE 29 28
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                26                 57 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                 28 
$`11P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3MO TCGA-D9-A3Z3 
       16.47        32.55        22.55        10.26         9.30         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EE-A29C TCGA-EE-A29D 
       48.79        35.80        39.19        25.15        37.97        11.15 
TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 
        1.08         8.12         8.84         8.09        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19L TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-GN-A262 TCGA-GN-A264 
        3.52        12.99         5.95        10.78        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A26A 
       16.21        12.16 

$`11P LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD 
       70.16        98.76        28.08         8.38        21.14        11.41 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV 
        6.35        15.25        45.70        13.32        24.00         5.39 
TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
        4.01        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S 
        5.13        38.63         4.41         9.47        12.03         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        6.48        11.31        25.28         8.94        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A 
       28.64        42.84        78.44         6.58         1.71        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A265 
        8.81        53.82         6.41         1.02        15.35        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.09        15.39        14.70 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.08               1.02 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.79              98.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            12.575             12.030 
[1] "1.1 - 48.8 (12.6)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11P LOSS MUTATED"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      9   26
  11P LOSS WILD-TYPE   26   86
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    26
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 26
  REGIONAL LYMPH NODE                                                                                      86
D55V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14   21
  11P LOSS WILD-TYPE   38   74
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               14                 38
  MALE                 21                 74
                    vv
clus                 M0 M1 M1A M1B M1C
  11P LOSS MUTATED   29  0   0   0   1
  11P LOSS WILD-TYPE 99  1   2   2   0
D55V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P LOSS MUTATED   13  0   2   5  0   1   1   2  5  1
  11P LOSS WILD-TYPE 64  2   4   7  1   3  10   2 11  1
D55V6, multiclass
D55V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       1        1        5        1         0
  11P LOSS WILD-TYPE           0      15        7        8       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED           3         1         1          2          5
  11P LOSS WILD-TYPE         5         3         7          3         11
                    vv
clus                 STAGE IIIC STAGE IV
  11P LOSS MUTATED            7        1
  11P LOSS WILD-TYPE         14        3
D55V8, multiclass

Clustering(56) Variable = 11q loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   11 15
  11Q LOSS WILD-TYPE 28 29
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                 57 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                15                 29 
$`11Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A3MO 
       16.47        32.55        98.76        22.55        10.26         9.30 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I8 TCGA-EE-A29C 
        2.86        48.79        35.80        39.19        25.15        37.97 
TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2A2 TCGA-EE-A2A5 
       11.15         1.08         8.12         8.84        23.90         9.67 
TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN TCGA-GN-A264 TCGA-GN-A267 
        3.52        12.99         1.71         5.95        31.33        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK 
       70.16        28.08         8.38        21.14        11.41         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        13.32        24.00         5.39         4.01 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IB 
       51.12        10.03        13.68         9.99        36.69        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
        6.64        19.36         7.00        17.56        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12        12.20         4.27        36.07         5.13 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T 
       38.63         4.41         9.47        12.03         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        8.09        11.31        25.28         8.94        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A1ZR 
       28.64        42.84        78.44         6.58        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       53.82        10.78         6.41         1.02        15.35        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       84.72        10.09        15.39 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.08               1.02 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             98.76              84.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.845             11.570 
[1] "1.1 - 98.8 (13.8)" "1.0 - 84.7 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
[1] "hr=" "1"  
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9   30
  11Q LOSS WILD-TYPE   26   82
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    30
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 26
  REGIONAL LYMPH NODE                                                                                      82
D56V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     15   24
  11Q LOSS WILD-TYPE   37   71
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               15                 37
  MALE                 24                 71
                    vv
clus                 M0 M1 M1A M1B M1C
  11Q LOSS MUTATED   32  0   1   0   1
  11Q LOSS WILD-TYPE 96  1   1   2   0
D56V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q LOSS MUTATED   17  0   3   6  0   1   1   2  4  1
  11Q LOSS WILD-TYPE 60  2   3   6  1   3  10   2 12  1
D56V6, multiclass
D56V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       2        1        6        1         0
  11Q LOSS WILD-TYPE           0      14        7        7       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED           3         2         1          3          5
  11Q LOSS WILD-TYPE         5         2         7          2         11
                    vv
clus                 STAGE IIIC STAGE IV
  11Q LOSS MUTATED            7        2
  11Q LOSS WILD-TYPE         14        2
D56V8, multiclass

Clustering(57) Variable = 12p loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  1
  12P LOSS WILD-TYPE 35 43
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 78 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 43 
$`12P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1I1 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A2A2 
       10.26        39.19         8.12         9.99        23.90 

$`12P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T 
        4.41         1.08         9.47        12.03         8.84         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
        8.09        11.31        25.28         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        16.21        15.39        12.16        14.70 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              8.12               1.02 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             39.19              98.76 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             10.26              12.18 
[1] "8.1 - 39.2 (10.3)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    5
  12P LOSS WILD-TYPE   32  107
                                                                                          clus
vv                                                                                         12P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     107
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    4
  12P LOSS WILD-TYPE   48   91
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                4                 48
  MALE                  4                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  12P LOSS MUTATED     7   0   0   0   1
  12P LOSS WILD-TYPE 121   1   2   2   0
D57V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P LOSS MUTATED    5  0   0   1  0   0   0   1  1  0
  12P LOSS WILD-TYPE 72  2   6  11  1   4  11   3 15  2
D57V6, multiclass
D57V7, 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         1
  12P LOSS WILD-TYPE           1      15        8       13       16         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED           2         0         0          0          1
  12P LOSS WILD-TYPE         6         4         8          5         15
                    vv
clus                 STAGE IIIC STAGE IV
  12P LOSS MUTATED            1        1
  12P LOSS WILD-TYPE         20        3
D57V8, multiclass

Clustering(58) Variable = 12q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    6  3
  12Q LOSS WILD-TYPE 33 41
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 9                 74 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 41 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
       16.47        45.70        39.19         8.12         9.99         8.09 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A3PL 
       23.90         9.67         1.71 

$`12Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       32.55        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
        8.38        21.14        11.41         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       24.00         9.30         5.39         4.01         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A0 
        1.08         9.47        12.03         8.84         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
       25.28         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A 
       28.64        42.84        78.44         6.58         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1.71               1.02 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             45.70              98.76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              9.99              12.18 
[1] "1.7 - 45.7 (10.0)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED"   "12Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7    8
  12Q LOSS WILD-TYPE   28  104
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 28
  REGIONAL LYMPH NODE                                                                                     104
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      8    7
  12Q LOSS WILD-TYPE   44   88
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                8                 44
  MALE                  7                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q LOSS MUTATED    12   0   1   0   1
  12Q LOSS WILD-TYPE 116   1   1   2   0
D58V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q LOSS MUTATED   10  0   0   1  0   0   0   1  2  0
  12Q LOSS WILD-TYPE 67  2   6  11  1   4  11   3 14  2
D58V6, multiclass
D58V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             0       1        1        2        2         1
  12Q LOSS WILD-TYPE           1      15        7       11       15         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED           1         1         0          0          1
  12Q LOSS WILD-TYPE         7         3         8          5         15
                    vv
clus                 STAGE IIIC STAGE IV
  12Q LOSS MUTATED            2        2
  12Q LOSS WILD-TYPE         19        2
D58V8, multiclass

Clustering(59) Variable = 13q loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    7  9
  13Q LOSS WILD-TYPE 32 35
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                16                 67 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                 35 
$`13Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 
       28.08         2.86        48.79        13.68         9.99        25.15 
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29N TCGA-EE-A29Q 
        6.64         1.12        37.97        11.15         9.47         8.12 
TCGA-EE-A29T TCGA-FR-A3YN TCGA-GN-A266 TCGA-GN-A26D 
        6.48         5.95        10.09        14.70 

$`13Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HW 
       13.32        24.00         9.30         5.39         4.01        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 
       51.12        10.03        39.19        36.69        22.36        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
        7.00        17.56        14.83        11.57         6.31        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        4.27        36.07         5.13        38.63         4.41         1.08 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.84         9.99         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 
       15.35        24.85        31.33        84.72        16.21        15.39 
TCGA-GN-A26A 
       12.16 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.12               1.02 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             48.79              98.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.04              12.99 
[1] "1.1 - 48.8 (10.0)" "1.0 - 98.8 (13.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
[1] "hr=" "1.5"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6   17
  13Q LOSS WILD-TYPE   29   95
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    17
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      95
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   15
  13Q LOSS WILD-TYPE   44   80
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                8                 44
  MALE                 15                 80
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q LOSS MUTATED    17   0   0   2   1
  13Q LOSS WILD-TYPE 111   1   2   0   0
D59V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q LOSS MUTATED    9  0   0   3  0   0   3   2  3  1
  13Q LOSS WILD-TYPE 68  2   6   9  1   4   8   2 13  1
D59V6, multiclass
D59V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       0        1        2        3         0
  13Q LOSS WILD-TYPE           1      16        7       11       14         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED           1         1         0          0          4
  13Q LOSS WILD-TYPE         7         3         8          5         12
                    vv
clus                 STAGE IIIC STAGE IV
  13Q LOSS MUTATED            3        2
  13Q LOSS WILD-TYPE         18        2
D59V8, multiclass

Clustering(60) Variable = 14q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    9 11
  14Q LOSS WILD-TYPE 30 33
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                20                 63 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                11                 33 
$`14Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-DA-A1HV TCGA-DA-A1HY 
       16.47        10.26        45.70        13.32        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29X TCGA-EE-A2A5 
       39.19        17.56         1.12        37.97         8.09         9.67 
TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F9 TCGA-GN-A264 TCGA-GN-A267 
        8.94         1.71         8.81        10.78        31.33        16.21 
TCGA-GN-A268 TCGA-GN-A26A 
       15.39        12.16 

$`14Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J8 
       32.55        70.16        98.76        28.08        22.55         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MO 
       21.14        11.41         6.35        15.25        24.00         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I2 
        5.39         4.01         2.86        35.80        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 TCGA-EE-A185 
        7.00        14.83        11.57         6.31        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
       36.07         5.13        11.15        38.63         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28        23.90         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN 
       12.99        28.64        42.84        78.44         6.58         5.95 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       72.16        53.82         6.41         1.02        15.35        24.85 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       84.72        10.09        14.70 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.12               1.02 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             51.12              98.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            14.355             11.570 
[1] "1.1 - 51.1 (14.4)" "1.0 - 98.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   25
  14Q LOSS WILD-TYPE   25   87
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               10
  REGIONAL LYMPH NODE                                                                                    25
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 25
  REGIONAL LYMPH NODE                                                                                      87
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12   23
  14Q LOSS WILD-TYPE   40   72
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               12                 40
  MALE                 23                 72
                    vv
clus                 M0 M1 M1A M1B M1C
  14Q LOSS MUTATED   32  0   1   0   1
  14Q LOSS WILD-TYPE 96  1   1   2   0
D60V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q LOSS MUTATED   20  0   3   3  0   0   1   2  5  0
  14Q LOSS WILD-TYPE 57  2   3   9  1   4  10   2 11  2
D60V6, multiclass
D60V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             0       4        1        3        8         0
  14Q LOSS WILD-TYPE           1      12        7       10        9         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED           2         1         2          2          2
  14Q LOSS WILD-TYPE         6         3         6          3         14
                    vv
clus                 STAGE IIIC STAGE IV
  14Q LOSS MUTATED            6        2
  14Q LOSS WILD-TYPE         15        2
D60V8, multiclass

Clustering(61) Variable = 15q loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    2  5
  15Q LOSS WILD-TYPE 37 39
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 39 
$`15Q LOSS MUTATED`
TCGA-D3-A3C6 TCGA-DA-A1I1 TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A2A5 TCGA-GN-A266 
       15.25        39.19         1.08        12.03         9.67        10.09 
TCGA-GN-A267 
       16.21 

$`15Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC 
       10.26         8.38        21.14        11.41         6.35        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         5.13        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        4.41         9.47         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D 
        8.09        11.31        25.28        23.90         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         1.02        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        15.39        12.16        14.70 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.08               1.02 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             39.19              98.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             12.03              12.18 
[1] "1.1 - 39.2 (12.0)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "15Q LOSS MUTATED"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    7
  15Q LOSS WILD-TYPE   30  105
                                                                                          clus
vv                                                                                         15Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     105
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    8
  15Q LOSS WILD-TYPE   48   87
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 48
  MALE                  8                 87
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q LOSS MUTATED     9   0   0   1   0
  15Q LOSS WILD-TYPE 119   1   2   1   1
D61V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q LOSS MUTATED    5  0   1   0  0   0   0   1  3  0
  15Q LOSS WILD-TYPE 72  2   5  12  1   4  11   3 13  2
D61V6, multiclass
D61V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       1        0        2        1         0
  15Q LOSS WILD-TYPE           1      15        8       11       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED           0         1         1          1          0
  15Q LOSS WILD-TYPE         8         3         7          4         16
                    vv
clus                 STAGE IIIC STAGE IV
  15Q LOSS MUTATED            2        0
  15Q LOSS WILD-TYPE         19        4
D61V8, multiclass

Clustering(62) Variable = 16p loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  6
  16P LOSS WILD-TYPE 38 38
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                 76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 38 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A29X 
       32.55        35.80        13.68         6.31        11.15         8.09 
TCGA-GN-A262 
       24.85 

$`16P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
       48.79        51.12        10.03        39.19         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       14.83        11.57         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
       12.03         8.12         8.84         9.99         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       25.28        23.90         9.67         8.94         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02        15.35        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        15.39        12.16        14.70 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              6.31               1.02 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.80              98.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            13.680             12.095 
[1] "6.3 - 35.8 (13.7)" "1.0 - 98.8 (12.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    8
  16P LOSS WILD-TYPE   34  104
                                                                                          clus
vv                                                                                         16P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         16P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     104
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    5
  16P LOSS WILD-TYPE   48   90
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 48
  MALE                  5                 90
                    vv
clus                  M0  M1 M1A M1B M1C
  16P LOSS MUTATED     8   0   0   0   0
  16P LOSS WILD-TYPE 120   1   2   2   1
D62V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P LOSS MUTATED    5  0   0   2  0   0   1   0  0  0
  16P LOSS WILD-TYPE 72  2   6  10  1   4  10   4 16  2
D62V6, multiclass
D62V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16P LOSS MUTATED             1       0        0        1        1         0
  16P LOSS WILD-TYPE           0      16        8       12       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED           2         0         0          0          1
  16P LOSS WILD-TYPE         6         4         8          5         15
                    vv
clus                 STAGE IIIC STAGE IV
  16P LOSS MUTATED            2        0
  16P LOSS WILD-TYPE         19        4
D62V8, multiclass

Clustering(63) Variable = 16q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    3 10
  16Q LOSS WILD-TYPE 36 34
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                13                 70 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                10                 34 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F8 
       32.55         2.86        35.80        13.68         9.99        14.83 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29X TCGA-EE-A2A5 TCGA-GN-A262 
        6.31         4.27        11.15         8.09         9.67        24.85 
TCGA-GN-A267 
       16.21 

$`16Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV 
       13.32        24.00         9.30         5.39         4.01        48.79 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       51.12        10.03        39.19        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17X TCGA-EE-A181 
        6.64        19.36         7.00        17.56        11.57         1.12 
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-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D 
        6.48        11.31        25.28        23.90         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 
       10.78         6.41         1.02        15.35        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        15.39        12.16        14.70 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2.86               1.02 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.80              98.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.15              12.18 
[1] "2.9 - 35.8 (11.2)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      5   15
  16Q LOSS WILD-TYPE   30   97
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      97
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7   13
  16Q LOSS WILD-TYPE   45   82
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                 45
  MALE                 13                 82
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q LOSS MUTATED    17   0   0   1   0
  16Q LOSS WILD-TYPE 111   1   2   1   1
D63V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q LOSS MUTATED    7  0   2   4  0   0   3   0  2  0
  16Q LOSS WILD-TYPE 70  2   4   8  1   4   8   4 14  2
D63V6, multiclass
D63V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             1       0        0        2        2         0
  16Q LOSS WILD-TYPE           0      16        8       11       15         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED           2         0         0          1          5
  16Q LOSS WILD-TYPE         6         4         8          4         11
                    vv
clus                 STAGE IIIC STAGE IV
  16Q LOSS MUTATED            3        0
  16Q LOSS WILD-TYPE         18        4
D63V8, multiclass

Clustering(64) Variable = 17p loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   11  9
  17P LOSS WILD-TYPE 28 35
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                20                 63 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 9                 35 
$`17P LOSS MUTATED`
TCGA-D3-A2J6 TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A3F3 
       10.26         9.30        48.79        35.80        51.12         7.00 
TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29S TCGA-EE-A29T 
        4.27        37.97         4.41         1.08         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-FR-A3YN TCGA-FS-A4F9 
        8.09        25.28        23.90         9.67         5.95        10.78 
TCGA-FW-A3R5 TCGA-GN-A266 
        1.02        10.09 

$`17P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1I0 
       13.32        24.00         5.39         4.01         2.86        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB 
       39.19        13.68         9.99        36.69        25.15        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
        6.64        19.36        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E 
        1.12        12.20        36.07         5.13        11.15        38.63 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2A0 TCGA-EE-A2A6 
        9.47        12.03         8.12         8.84        11.31         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       78.44         6.58         1.71        72.16         8.81        53.82 
TCGA-FS-A4FC TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        6.41        15.35        24.85        31.33        84.72        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              1.02               1.12 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.12              98.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.83              13.68 
[1] "1.0 - 51.1 (9.8)"  "1.1 - 98.8 (13.7)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      5   28
  17P LOSS WILD-TYPE   30   84
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    28
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      84
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10   23
  17P LOSS WILD-TYPE   42   72
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               10                 42
  MALE                 23                 72
                    vv
clus                 M0 M1 M1A M1B M1C
  17P LOSS MUTATED   30  0   0   1   1
  17P LOSS WILD-TYPE 98  1   2   1   0
D64V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P LOSS MUTATED   17  0   1   2  1   1   2   2  5  1
  17P LOSS WILD-TYPE 60  2   5  10  0   3   9   2 11  1
D64V6, multiclass
D64V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             0       4        3        5        1         2
  17P LOSS WILD-TYPE           1      12        5        8       16         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED           2         0         2          1          5
  17P LOSS WILD-TYPE         6         4         6          4         11
                    vv
clus                 STAGE IIIC STAGE IV
  17P LOSS MUTATED            4        1
  17P LOSS WILD-TYPE         17        3
D64V8, multiclass

Clustering(65) Variable = 17q loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    2  4
  17Q LOSS WILD-TYPE 37 40
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 77 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                 40 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A29X TCGA-ER-A19L TCGA-FS-A4F9 
       10.26        35.80        37.97         8.09        12.99        10.78 

$`17Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.79        51.12        10.03        39.19        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27        36.07         5.13        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        6.48        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        3.52        11.11         4.18        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
        6.58         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              8.09               1.02 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             37.97              98.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            11.885             12.160 
[1] "8.1 - 38.0 (11.9)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   11
  17Q LOSS WILD-TYPE   34  101
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     101
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    8
  17Q LOSS WILD-TYPE   48   87
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                 48
  MALE                  8                 87
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q LOSS MUTATED    10   0   0   0   1
  17Q LOSS WILD-TYPE 118   1   2   2   0
D65V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q LOSS MUTATED    6  0   1   1  0   1   0   1  1  0
  17Q LOSS WILD-TYPE 71  2   5  11  1   3  11   3 15  2
D65V6, multiclass
D65V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             0       1        1        2        0         1
  17Q LOSS WILD-TYPE           1      15        7       11       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED           1         0         0          1          2
  17Q LOSS WILD-TYPE         7         4         8          4         14
                    vv
clus                 STAGE IIIC STAGE IV
  17Q LOSS MUTATED            1        1
  17Q LOSS WILD-TYPE         20        3
D65V8, multiclass

Clustering(66) Variable = 18p loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    5  7
  18P LOSS WILD-TYPE 34 37
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 71 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 37 
$`18P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1I2 TCGA-DA-A1I7 
       16.47        70.16        15.25        48.79        13.68        36.69 
TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29T TCGA-EE-A29X TCGA-FS-A1ZR 
       17.56        36.07        11.15         6.48         8.09         8.81 

$`18P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        98.76        28.08        22.55        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       21.14        11.41         6.35        45.70        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY 
        9.30         5.39         4.01         2.86        35.80        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       10.03        39.19         9.99        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
       19.36         7.00        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H 
       12.20         4.27         5.13        37.97        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D 
       11.31        25.28        23.90         9.67         8.94         3.52 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 
        6.58         1.71         5.95        72.16        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              6.48               1.02 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             70.16              98.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             15.86              11.57 
[1] "6.5 - 70.2 (15.9)" "1.0 - 98.8 (11.6)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8   18
  18P LOSS WILD-TYPE   27   94
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    18
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 27
  REGIONAL LYMPH NODE                                                                                      94
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     11   15
  18P LOSS WILD-TYPE   41   80
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               11                 41
  MALE                 15                 80
                    vv
clus                  M0  M1 M1A M1B M1C
  18P LOSS MUTATED    25   0   0   0   0
  18P LOSS WILD-TYPE 103   1   2   2   1
D66V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P LOSS MUTATED   12  0   2   2  0   1   3   1  2  2
  18P LOSS WILD-TYPE 65  2   4  10  1   3   8   3 14  0
D66V6, multiclass
D66V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             0       1        2        2        7         0
  18P LOSS WILD-TYPE           1      15        6       11       10         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED           0         0         2          1          4
  18P LOSS WILD-TYPE         8         4         6          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  18P LOSS MUTATED            4        0
  18P LOSS WILD-TYPE         17        4
D66V8, multiclass

Clustering(67) Variable = 18q loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  8
  18Q LOSS WILD-TYPE 34 36
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                13                 70 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 36 
$`18Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-DA-A1HV 
       16.47        70.16        22.55        15.25        13.32        48.79 
TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29T 
       13.68        36.69        17.56        36.07        11.15         6.48 
TCGA-EE-A29X 
        8.09 

$`18Q LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 
       32.55        98.76        28.08        10.26         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
       11.41         6.35        45.70        24.00         9.30         5.39 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
        4.01         2.86        35.80        51.12        10.03        39.19 
TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
        9.99        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        38.63         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.12         8.84         9.99        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        1.02        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        15.39        12.16        14.70 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              6.48               1.02 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             70.16              98.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             16.47              11.36 
[1] "6.5 - 70.2 (16.5)" "1.0 - 98.8 (11.4)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D67V2, continuous
D67V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6   18
  18Q LOSS WILD-TYPE   29   94
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    18
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      94
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     10   14
  18Q LOSS WILD-TYPE   42   81
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               10                 42
  MALE                 14                 81
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q LOSS MUTATED    23   0   0   1   0
  18Q LOSS WILD-TYPE 105   1   2   1   1
D67V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q LOSS MUTATED    9  0   2   3  0   2   3   1  3  1
  18Q LOSS WILD-TYPE 68  2   4   9  1   2   8   3 13  1
D67V6, multiclass
D67V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             0       0        2        2        5         0
  18Q LOSS WILD-TYPE           1      16        6       11       12         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED           0         0         3          1          5
  18Q LOSS WILD-TYPE         8         4         5          4         11
                    vv
clus                 STAGE IIIC STAGE IV
  18Q LOSS MUTATED            4        0
  18Q LOSS WILD-TYPE         17        4
D67V8, multiclass

Clustering(68) Variable = 19p loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    3  6
  19P LOSS WILD-TYPE 36 38
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                 74 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 38 
$`19P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I8 
       16.47        22.55         2.86        48.79        35.80        25.15 
TCGA-EE-A29H TCGA-EE-A29X TCGA-EE-A2A0 
        4.41         8.09        11.31 

$`19P LOSS WILD-TYPE`
TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2J8 
       32.55        70.16        98.76        28.08        10.26         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       21.14        11.41         6.35        15.25        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 
       24.00         9.30         5.39         4.01        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19        13.68         9.99        36.69        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       19.36         7.00        17.56        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C 
        1.12        12.20         4.27        36.07         5.13        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15        38.63         1.08         9.47        12.03         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99         6.48        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
        8.94         3.52        11.11         4.18        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       42.84        78.44         6.58         1.71         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 
        8.81        53.82        10.78         6.41         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       24.85        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.86               1.02 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.79              98.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            16.470             12.095 
[1] "2.9 - 48.8 (16.5)" "1.0 - 98.8 (12.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19P LOSS MUTATED"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19P LOSS MUTATED"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19P LOSS MUTATED"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2   12
  19P LOSS WILD-TYPE   33  100
                                                                                          clus
vv                                                                                         19P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     100
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10    4
  19P LOSS WILD-TYPE   42   91
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                 42
  MALE                  4                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  19P LOSS MUTATED    12   0   0   1   1
  19P LOSS WILD-TYPE 116   1   2   1   0
D68V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P LOSS MUTATED    4  0   1   2  0   1   2   1  3  0
  19P LOSS WILD-TYPE 73  2   5  10  1   3   9   3 13  2
D68V6, multiclass
D68V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             0       0        1        1        0         1
  19P LOSS WILD-TYPE           1      16        7       12       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED           0         1         1          0          5
  19P LOSS WILD-TYPE         8         3         7          5         11
                    vv
clus                 STAGE IIIC STAGE IV
  19P LOSS MUTATED            2        1
  19P LOSS WILD-TYPE         19        3
D68V8, multiclass

Clustering(69) Variable = 19q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  4
  19Q LOSS WILD-TYPE 34 40
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 9                 74 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 40 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I8 TCGA-EE-A29H TCGA-EE-A29S 
       22.55         2.86        48.79        25.15         4.41         9.99 
TCGA-EE-A29X TCGA-GN-A26A TCGA-GN-A26D 
        8.09        12.16        14.70 

$`19Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        28.08        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HW 
       13.32        24.00         9.30         5.39         4.01        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       51.12        10.03        39.19        13.68         9.99        36.69 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       22.36         6.64        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.12        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
        5.13        37.97        11.15        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A1 
       12.03         8.12         8.84         6.48        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       23.90         9.67         8.94         3.52        11.11         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
       12.99        28.64        42.84        78.44         6.58         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
        5.95        72.16         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        1.02        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2.86               1.02 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.79              98.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            12.160             12.115 
[1] "2.9 - 48.8 (12.2)" "1.0 - 98.8 (12.1)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3   12
  19Q LOSS WILD-TYPE   32  100
                                                                                          clus
vv                                                                                         19Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     100
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8    7
  19Q LOSS WILD-TYPE   44   88
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                 44
  MALE                  7                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q LOSS MUTATED    10   0   0   1   1
  19Q LOSS WILD-TYPE 118   1   2   1   0
D69V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q LOSS MUTATED    4  0   2   1  0   1   2   1  2  0
  19Q LOSS WILD-TYPE 73  2   4  11  1   3   9   3 14  2
D69V6, multiclass
D69V7, 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         1
  19Q LOSS WILD-TYPE           1      16        7       12       17         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED           0         1         1          1          4
  19Q LOSS WILD-TYPE         8         3         7          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  19Q LOSS MUTATED            1        1
  19Q LOSS WILD-TYPE         20        3
D69V8, multiclass

Clustering(70) Variable = 20p loss mutation analysis
D70V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  2
  20P LOSS WILD-TYPE 35 42
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 77 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 42 
$`20P LOSS MUTATED`
TCGA-D3-A3CF TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-EE-A29E TCGA-ER-A3PL TCGA-FS-A1ZR 
       24.00        48.79        39.19        38.63         1.71         8.81 

$`20P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 
       10.26         8.38        21.14        11.41         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        13.32         9.30         5.39         4.01         2.86 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 
       35.80        51.12        10.03        13.68         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       25.15        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.12        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       36.07         5.13        37.97        11.15         4.41         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        8.09        11.31        25.28        23.90         9.67         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        3.52        11.11         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 
       78.44         6.58         5.95        72.16        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.71               1.02 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             48.79              98.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            31.315             12.030 
[1] "1.7 - 48.8 (31.3)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"20P LOSS WILD-TYPE"   "20P LOSS MUTATED" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D70V2, continuous
D70V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    3
  20P LOSS WILD-TYPE   32  109
                                                                                          clus
vv                                                                                         20P LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         20P LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     109
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    4
  20P LOSS WILD-TYPE   50   91
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 50
  MALE                  4                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  20P LOSS MUTATED     5   0   1   0   0
  20P LOSS WILD-TYPE 123   1   1   2   1
D70V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P LOSS MUTATED    2  0   0   1  0   0   1   0  2  0
  20P LOSS WILD-TYPE 75  2   6  11  1   4  10   4 14  2
D70V6, multiclass
D70V7, 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           1      16        8       13       16         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED           0         0         0          0          2
  20P LOSS WILD-TYPE         8         4         8          5         14
                    vv
clus                 STAGE IIIC STAGE IV
  20P LOSS MUTATED            2        1
  20P LOSS WILD-TYPE         19        3
D70V8, multiclass

Clustering(71) Variable = 21q loss mutation analysis
D71V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    4  4
  21Q LOSS WILD-TYPE 35 40
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 75 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 40 
$`21Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A29H TCGA-EE-A2A2 TCGA-EE-A2A6 
       32.55         1.12        36.07         4.41        23.90         8.94 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        15.39 

$`21Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        70.16        98.76        28.08        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A183 
        7.00        17.56        14.83        11.57         6.31        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        4.27         5.13        37.97        11.15        38.63         1.08 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
        9.47        12.03         8.12         8.84         9.99         6.48 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F 
        8.09        11.31        25.28         9.67         3.52        11.11 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
        4.18        12.99        28.64        42.84        78.44         6.58 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 
        1.71         5.95        72.16         8.81        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        12.16        14.70 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.12               1.02 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             36.07              98.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.74              12.16 
[1] "1.1 - 36.1 (12.7)" "1.0 - 98.8 (12.2)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   15
  21Q LOSS WILD-TYPE   32   97
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      97
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7   11
  21Q LOSS WILD-TYPE   45   84
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                7                 45
  MALE                 11                 84
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q LOSS MUTATED    17   0   0   0   0
  21Q LOSS WILD-TYPE 111   1   2   2   1
D71V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q LOSS MUTATED   14  0   1   1  0   0   1   0  0  0
  21Q LOSS WILD-TYPE 63  2   5  11  1   4  10   4 16  2
D71V6, multiclass
D71V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  21Q LOSS MUTATED             1       2        3        0        6         0
  21Q LOSS WILD-TYPE           0      14        5       13       11         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED           2         0         0          1          1
  21Q LOSS WILD-TYPE         6         4         8          4         15
                    vv
clus                 STAGE IIIC STAGE IV
  21Q LOSS MUTATED            1        0
  21Q LOSS WILD-TYPE         20        4
D71V8, multiclass

Clustering(72) Variable = 22q loss mutation analysis
D72V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    3  3
  22Q LOSS WILD-TYPE 36 41
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 6                 77 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 41 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-DA-A1I2 TCGA-EE-A29C TCGA-EE-A2A6 TCGA-ER-A19D TCGA-FS-A4F0 
       28.08        13.68        37.97         8.94         3.52        53.82 

$`22Q LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A2J6 
       16.47        32.55        70.16        98.76        22.55        10.26 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
        8.38        21.14        11.41         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        39.19         9.99 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.27        36.07         5.13        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        1.08         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        6.48         8.09        11.31        25.28        23.90         9.67 
TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
       11.11         4.18        12.99        28.64        42.84        78.44 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F9 
        6.58         1.71         5.95        72.16         8.81        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        6.41         1.02        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        16.21        15.39        12.16        14.70 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              3.52               1.02 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             53.82              98.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             20.88              12.03 
[1] "3.5 - 53.8 (20.9)" "1.0 - 98.8 (12.0)"
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q1         TCGA-D3-A1Q5         TCGA-D3-A1Q6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A1Q7         TCGA-D3-A1Q8         TCGA-D3-A1Q9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A2J8         TCGA-D3-A2J9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JK         TCGA-D3-A3C6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CC         TCGA-D3-A3CE         TCGA-D3-A3CF 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3MO         TCGA-D3-A3MV         TCGA-D9-A3Z1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z3         TCGA-DA-A1HV         TCGA-DA-A1HW 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HY         TCGA-DA-A1I0         TCGA-DA-A1I1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I2         TCGA-DA-A1I4         TCGA-DA-A1I7 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I8         TCGA-DA-A1IB         TCGA-DA-A1IC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F2         TCGA-DA-A3F3         TCGA-DA-A3F5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A3F8         TCGA-EE-A17X         TCGA-EE-A17Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A181         TCGA-EE-A183         TCGA-EE-A185 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20B         TCGA-EE-A20F         TCGA-EE-A29C 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29N         TCGA-EE-A29P 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29Q         TCGA-EE-A29R         TCGA-EE-A29S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29T         TCGA-EE-A29X         TCGA-EE-A2A0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A1         TCGA-EE-A2A2         TCGA-EE-A2A5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A6         TCGA-ER-A19D         TCGA-ER-A19F 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19J         TCGA-ER-A19L         TCGA-ER-A19M 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19N         TCGA-ER-A1A1         TCGA-ER-A3ET 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A3PL         TCGA-FR-A3YN         TCGA-FR-A44A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A1ZR         TCGA-FS-A4F0         TCGA-FS-A4F9 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3R5         TCGA-GN-A261 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A262         TCGA-GN-A264         TCGA-GN-A265 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A266         TCGA-GN-A267         TCGA-GN-A268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D72V2, continuous
D72V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5    7
  22Q LOSS WILD-TYPE   30  105
                                                                                          clus
vv                                                                                         22Q LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     105
D72V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    6
  22Q LOSS WILD-TYPE   46   89
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 46
  MALE                  6                 89
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q LOSS MUTATED    11   0   0   1   0
  22Q LOSS WILD-TYPE 117   1   2   1   1
D72V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q LOSS MUTATED    8  0   1   1  0   0   1   0  1  0
  22Q LOSS WILD-TYPE 69  2   5  11  1   4  10   4 15  2
D72V6, multiclass
D72V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       3        1        3        0         0
  22Q LOSS WILD-TYPE           1      13        7       10       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED           1         0         0          0          1
  22Q LOSS WILD-TYPE         7         4         8          5         15
                    vv
clus                 STAGE IIIC STAGE IV
  22Q LOSS MUTATED            1        1
  22Q LOSS WILD-TYPE         20        3
D72V8, multiclass

Clustering(73) Variable = Xq loss mutation analysis
D73V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  1
  XQ LOSS WILD-TYPE 37 43
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                3                80 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                43 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-EE-A29H TCGA-GN-A262 
       15.25         4.41        24.85 

$`XQ LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1Q9 
       16.47        32.55        70.16        98.76        28.08        22.55 
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JK TCGA-D3-A3CC 
       10.26         8.38        21.14        11.41         6.35        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       13.32        24.00         9.30         5.39         4.01         2.86 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
       48.79        35.80        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        36.69        25.15        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 
        7.00        17.56        14.83        11.57         6.31         1.12 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
       12.20         4.27        36.07         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
       38.63         1.08         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
        9.67         8.94         3.52        11.11         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       28.64        42.84        78.44         6.58         1.71         5.95 
TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
       72.16         8.81        53.82        10.78         6.41         1.02 
TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        31.33        84.72        10.09        16.21        15.39 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.41              1.02 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            24.85             98.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           15.250            12.095 
[1] "4.4 - 24.9 (15.2)" "1.0 - 98.8 (12.1)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"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-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF        TCGA-D3-A3MO 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I7        TCGA-DA-A1I8 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IB        TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F5        TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A181        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A29C        TCGA-EE-A29D        TCGA-EE-A29E 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29N        TCGA-EE-A29P 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29Q        TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F9 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3R5        TCGA-GN-A261        TCGA-GN-A262 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" 
       TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1    3
  XQ LOSS WILD-TYPE   34  109
                                                                                          clus
vv                                                                                         XQ LOSS MUTATED
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         XQ LOSS WILD-TYPE
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    109
D73V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      4    0
  XQ LOSS WILD-TYPE   48   95
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               4                48
  MALE                 0                95
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ LOSS MUTATED     3   0   0   0   0
  XQ LOSS WILD-TYPE 125   1   2   2   1
D73V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  XQ LOSS MUTATED    3  0   0   0  0   0   0   0  0  0
  XQ LOSS WILD-TYPE 74  2   6  12  1   4  11   4 16  2
D73V6, multiclass
D73V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ LOSS MUTATED             0       1        1        1        0         0
  XQ LOSS WILD-TYPE           1      15        7       12       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XQ LOSS MUTATED           0         0         0          0          0
  XQ LOSS WILD-TYPE         8         4         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  XQ LOSS MUTATED            0        0
  XQ LOSS WILD-TYPE         21        4
D73V8, 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")
