
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-All_Metastatic/3164316/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Metastatic/3180574/SKCM-All_Metastatic.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SKCM-All_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-All_Metastatic"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=180, in cluster file=244, common to both=173
[1] "Reduce the number of clustering variables from 80 to 77."
[1]  77 173
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               22               151 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               22               151 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               59               114 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               59               114 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18               155 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               18               155 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               16               157 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               16               157 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               18               155 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               18               155 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               150 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               23               150 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               156 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               17               156 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               160 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               160 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19               154 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19               154 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               166 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7               166 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               58               115 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               58               115 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               12               161 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               12               161 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               73               100 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               73               100 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               74                99 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               74                99 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35               138 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35               138 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               54               119 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               54               119 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               170 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3               170 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               170 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               170 
[1] "11p gain mutation analysis"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                162 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                11                162 
[1] "11q gain mutation analysis"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                165 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                165 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                154 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                154 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                166 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                166 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                143 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                30                143 
[1] "14q gain mutation analysis"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                159 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                14                159 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                147 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                147 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                160 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                160 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                161 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                161 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                159 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                14                159 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                151 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                22                151 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                151 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                151 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                161 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                12                161 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                162 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                162 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                158 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                15                158 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                53                120 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                53                120 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                65                108 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                65                108 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                152 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                152 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                46                127 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                46                127 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               170 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3               170 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               160 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               160 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               167 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6               167 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               158 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               15               158 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               159 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               159 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               161 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               161 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               161 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               12               161 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19               154 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               19               154 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               18               155 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               18               155 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               150 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               150 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               136 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               37               136 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               156 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17               156 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               104 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               69               104 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               170 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               170 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               170 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               170 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               22               151 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               22               151 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               170 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3               170 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              100                73 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               75                98 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               75                98 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                77                 96 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                77                 96 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                 89 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                 89 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                45                128 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                45                128 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                48                125 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                48                125 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                163 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                10                163 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                154 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                19                154 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                147 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                26                147 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                42                131 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                42                131 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                162 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                11                162 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                159 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                159 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                31                142 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                31                142 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                38                135 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                38                135 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                156 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                156 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                35                138 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                35                138 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                140 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                140 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                158 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                15                158 
[1] "19q loss mutation analysis"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                16                157 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                16                157 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                166 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                166 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                21                152 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                21                152 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                160 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                13                160 
[1] "Xq loss mutation analysis"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               167 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6               167 
[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 173 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-A2JF TCGA-D3-A2JK 
          NA           NA           NA           NA          939           NA 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
          NA         1390           NA           NA           NA          164 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 
          NA           NA           NA           NA          122           87 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        1484           NA         1555           NA         1192           NA 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
          NA         1354         1116           NA           NA          680 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X 
          NA          589           NA          534          451           NA 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
          NA           NA           NA           NA           NA         1097 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
         156           NA           NA         1155           NA         1175 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
         134           NA          825           NA          366          247 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
         269          304          197           NA           NA           NA 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC 
         769          727           NA          272           NA           NA 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A2MU 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A3AG TCGA-EE-A3AH TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL 
          NA         1303           NA         2386          200           52 
TCGA-FR-A3YN TCGA-FR-A3YO TCGA-FR-A44A TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
         181           NA         2195           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
        1637           NA          328          195            6           31 
TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
           4           NA           NA          756           NA         2577 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=64,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=27,	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  14   3  18  16   6   4  22  13   5   7  27   1  12 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 173 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=64, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=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  6
  1P GAIN WILD-TYPE 40 44
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                84 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                6                44 
$`1P GAIN MUTATED`
TCGA-DA-A1IC TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19F 
        6.64        11.15        38.63         1.08         8.84        11.11 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-GN-A266 TCGA-GN-A26A 
        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-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
       15.25        45.70        13.32        24.00         9.30         5.39 
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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.93        22.36        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H 
       36.07         5.13         8.81         7.96        37.97         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.47        12.03         8.12         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        8.94         3.52         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
       78.44         1.71        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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              0.13 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            38.63             98.76 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            9.465            12.595 
[1] "1.1 - 38.6 (9.5)"  "0.1 - 98.8 (12.6)"
       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 WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1P GAIN MUTATED" "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 WILD-TYPE" 
       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-A4F2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-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 WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1P GAIN MUTATED" "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 WILD-TYPE" 
       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-A4F2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-D3-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 WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1P GAIN MUTATED" "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 WILD-TYPE" 
       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-A4F2 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P GAIN MUTATED                    2             0
  1P GAIN WILD-TYPE                 23             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P GAIN MUTATED                                                                                          7
  1P GAIN WILD-TYPE                                                                                       28
                   vv
clus                REGIONAL LYMPH NODE
  1P GAIN MUTATED                    13
  1P GAIN WILD-TYPE                  99
D1V3, multiclass
                                                                                          clus
vv                                                                                         1P GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               7
  REGIONAL LYMPH NODE                                                                                   13
                                                                                          clus
vv                                                                                         1P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      23
  PRIMARY TUMOR                                                                                            1
  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     10   12
  1P GAIN WILD-TYPE   57   94
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              10                57
  MALE                12                94
                   vv
clus                 M0  M1 M1A M1B M1C
  1P GAIN MUTATED    21   0   0   0   0
  1P GAIN WILD-TYPE 129   2   2   2   2
D1V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P GAIN MUTATED   12  0   3   3  0   1   0   1  1  0
  1P GAIN WILD-TYPE 83  2   4  13  1   3  11   4 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       2        4        2        1         0
  1P GAIN WILD-TYPE           4      15        6       12       18         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P GAIN MUTATED           0         2         0          3          3
  1P GAIN WILD-TYPE        10         6         9          3         15
                   vv
clus                STAGE IIIC STAGE IV
  1P GAIN MUTATED            3        0
  1P GAIN WILD-TYPE         20        6
D1V8, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   15 17
  1Q GAIN WILD-TYPE 29 33
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                62 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17                33 
$`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-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC 
        2.86        39.19         9.99        44.52         4.93         6.64 
TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A20B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        7.00         6.31        36.07        11.15        38.63         1.08 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
        8.84         9.99        25.28         8.94         3.52        11.11 
TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-GN-A266 TCGA-GN-A267 
        6.58         1.71         5.95        72.16        10.09        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       21.14        30.87         6.35        15.25        45.70        24.00 
TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 
        4.01        48.79        35.80        51.12        10.03        13.68 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       36.69        25.15        22.36        19.36        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         1.12         1.35        12.20         4.27         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        8.81         7.96        37.97         4.41        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.12         6.48         2.43         8.09        11.31 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       23.90         9.67         4.18        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       78.44         8.81        53.82         3.22        10.78         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
        0.20         1.02         0.13        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A268 
       84.72        15.39 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.08              0.13 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            72.16             98.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            9.990            14.255 
[1] "1.1 - 72.2 (10.0)" "0.1 - 98.8 (14.3)"
       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-A2JF        TCGA-D3-A2JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "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 WILD-TYPE" 
       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-A4F2 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "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 WILD-TYPE" 
       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-A4F2 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "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 WILD-TYPE" 
       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-A4F2 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q GAIN MUTATED                   12             0
  1Q GAIN WILD-TYPE                 13             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q GAIN MUTATED                                                                                         15
  1Q GAIN WILD-TYPE                                                                                       20
                   vv
clus                REGIONAL LYMPH NODE
  1Q GAIN MUTATED                    32
  1Q GAIN WILD-TYPE                  80
D2V3, multiclass
                                                                                          clus
vv                                                                                         1Q GAIN MUTATED
  DISTANT METASTASIS                                                                                    12
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              15
  REGIONAL LYMPH NODE                                                                                   32
                                                                                          clus
vv                                                                                         1Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      13
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                20
  REGIONAL LYMPH NODE                                                                                     80
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     23   36
  1Q GAIN WILD-TYPE   44   70
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              23                44
  MALE                36                70
                   vv
clus                M0 M1 M1A M1B M1C
  1Q GAIN MUTATED   52  0   1   0   1
  1Q GAIN WILD-TYPE 98  2   1   2   1
D2V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q GAIN MUTATED   33  0   3   8  0   3   2   3  3  0
  1Q GAIN WILD-TYPE 62  2   4   8  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             1       2        5        6        6         2
  1Q GAIN WILD-TYPE           3      15        5        8       13         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q GAIN MUTATED           4         4         3          4          8
  1Q GAIN WILD-TYPE         6         4         6          2         10
                   vv
clus                STAGE IIIC STAGE IV
  1Q GAIN MUTATED            6        2
  1Q GAIN WILD-TYPE         17        4
D2V8, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    5  8
  2P GAIN WILD-TYPE 39 42
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                81 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                42 
$`2P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EE-A20H 
       16.47        70.16        22.55        11.41         5.39         8.81 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N TCGA-FR-A3YN 
        7.96        11.15         1.08         8.84        42.84         5.95 
TCGA-FR-A44A 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       30.87         6.35        15.25        45.70        13.32        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-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       12.20         4.27        36.07         5.13        37.97        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        4.41        27.12         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         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-FS-A1ZR TCGA-FS-A4F0 
       28.64        78.44         6.58         1.71         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
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 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.08              0.13 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            72.16             98.76 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            11.15             12.03 
[1] "1.1 - 72.2 (11.2)" "0.1 - 98.8 (12.0)"
       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-A2JF        TCGA-D3-A2JK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P GAIN MUTATED                    3             0
  2P GAIN WILD-TYPE                 22             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P GAIN MUTATED                                                                                          5
  2P GAIN WILD-TYPE                                                                                       30
                   vv
clus                REGIONAL LYMPH NODE
  2P GAIN MUTATED                    10
  2P GAIN WILD-TYPE                 102
D3V3, multiclass
                                                                                          clus
vv                                                                                         2P GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         2P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    102
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5   13
  2P GAIN WILD-TYPE   62   93
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5                62
  MALE                13                93
                   vv
clus                 M0  M1 M1A M1B M1C
  2P GAIN MUTATED    17   0   0   0   0
  2P GAIN WILD-TYPE 133   2   2   2   2
D3V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P GAIN MUTATED    8  0   1   4  0   2   0   0  2  0
  2P GAIN WILD-TYPE 87  2   6  12  1   2  11   5 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       1        1        1        2         2
  2P GAIN WILD-TYPE           4      16        9       13       17         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2P GAIN MUTATED           0         1         1          1          2
  2P GAIN WILD-TYPE        10         7         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  2P GAIN MUTATED            5        0
  2P GAIN WILD-TYPE         18        6
D3V8, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5  7
  2Q GAIN WILD-TYPE 39 43
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12                82 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                43 
$`2Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-EE-A20H 
       16.47        70.16        22.55        11.41         5.39         8.81 
TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29R TCGA-ER-A19N TCGA-FR-A3YN TCGA-FR-A44A 
        7.96         1.08         8.84        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       30.87         6.35        15.25        45.70        13.32        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-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41        27.12         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FS-A1ZR 
       12.99        28.64        78.44         6.58         1.71         8.81 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.08              0.13 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            72.16             98.76 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           10.125            11.800 
[1] "1.1 - 72.2 (10.1)" "0.1 - 98.8 (11.8)"
       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-A2JF        TCGA-D3-A2JK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "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 WILD-TYPE" "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-A4F2 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q GAIN MUTATED                    2             0
  2Q GAIN WILD-TYPE                 23             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q GAIN MUTATED                                                                                          5
  2Q GAIN WILD-TYPE                                                                                       30
                   vv
clus                REGIONAL LYMPH NODE
  2Q GAIN MUTATED                     9
  2Q GAIN WILD-TYPE                 103
D4V3, multiclass
                                                                                          clus
vv                                                                                         2Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         2Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      23
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    103
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   11
  2Q GAIN WILD-TYPE   62   95
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                62
  MALE                11                95
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q GAIN MUTATED    15   0   0   0   0
  2Q GAIN WILD-TYPE 135   2   2   2   2
D4V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q GAIN MUTATED    7  0   1   3  0   2   0   0  2  0
  2Q GAIN WILD-TYPE 88  2   6  13  1   2  11   5 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       1        1        1        1         2
  2Q GAIN WILD-TYPE           4      16        9       13       18         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  2Q GAIN MUTATED           0         1         1          1          2
  2Q GAIN WILD-TYPE        10         7         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  2Q GAIN MUTATED            4        0
  2Q GAIN WILD-TYPE         19        6
D4V8, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    7  6
  3P GAIN WILD-TYPE 37 44
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                81 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                44 
$`3P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MV TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A20H 
       30.87         5.39         4.93         7.00        17.56         8.81 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A3ET TCGA-FS-A4F2 
        1.08        27.12         8.84         6.48         6.58         3.22 
TCGA-GN-A266 
       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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       19.36        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C 
       12.20         4.27        36.07         5.13         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       11.15        38.63         4.41         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         2.43         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-A3PL TCGA-FR-A3YN TCGA-FR-A44A 
       28.64        42.84        78.44         1.71         5.95        72.16 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
        8.81        53.82        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.13        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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.08              0.13 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            30.87             98.76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              7.0              12.2 
[1] "1.1 - 30.9 (7.0)"  "0.1 - 98.8 (12.2)"
       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-A2JF        TCGA-D3-A2JK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       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-A4F2 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D5V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P GAIN MUTATED                    6             1
  3P GAIN WILD-TYPE                 19             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P GAIN MUTATED                                                                                          5
  3P GAIN WILD-TYPE                                                                                       30
                   vv
clus                REGIONAL LYMPH NODE
  3P GAIN MUTATED                     6
  3P GAIN WILD-TYPE                 106
D5V3, multiclass
                                                                                          clus
vv                                                                                         3P GAIN MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         3P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      19
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    106
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    9
  3P GAIN WILD-TYPE   58   97
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9                58
  MALE                 9                97
                   vv
clus                 M0  M1 M1A M1B M1C
  3P GAIN MUTATED    17   0   0   0   0
  3P GAIN WILD-TYPE 133   2   2   2   2
D5V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P GAIN MUTATED    8  0   2   2  0   1   1   0  2  1
  3P GAIN WILD-TYPE 87  2   5  14  1   3  10   5 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             1       1        2        1        1         1
  3P GAIN WILD-TYPE           3      16        8       13       18         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P GAIN MUTATED           0         1         0          1          4
  3P GAIN WILD-TYPE        10         7         9          5         14
                   vv
clus                STAGE IIIC STAGE IV
  3P GAIN MUTATED            3        0
  3P GAIN WILD-TYPE         20        6
D5V8, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    8  8
  3Q GAIN WILD-TYPE 36 42
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               16                78 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                42 
$`3Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3MV TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 
       30.87         5.39         4.93         7.00        17.56         1.35 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19M 
        5.13         8.81        27.12         8.84         6.48        28.64 
TCGA-ER-A3ET TCGA-FS-A4F2 TCGA-GN-A266 TCGA-GN-A26A 
        6.58         3.22        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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A183 
       19.36        14.83        11.57         6.31         1.12        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.27        36.07         7.96        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-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         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-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       78.44         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1.35              0.13 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            30.87             98.76 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            7.905            12.595 
[1] "1.4 - 30.9 (7.9)"  "0.1 - 98.8 (12.6)"
       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-A2JF        TCGA-D3-A2JK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4F2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4F2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       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-A4F2 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D6V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q GAIN MUTATED                    7             1
  3Q GAIN WILD-TYPE                 18             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q GAIN MUTATED                                                                                          6
  3Q GAIN WILD-TYPE                                                                                       29
                   vv
clus                REGIONAL LYMPH NODE
  3Q GAIN MUTATED                     9
  3Q GAIN WILD-TYPE                 103
D6V3, multiclass
                                                                                          clus
vv                                                                                         3Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     7
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         3Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      18
  PRIMARY TUMOR                                                                                            0
  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     11   12
  3Q GAIN WILD-TYPE   56   94
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              11                56
  MALE                12                94
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q GAIN MUTATED    22   0   0   0   0
  3Q GAIN WILD-TYPE 128   2   2   2   2
D6V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q GAIN MUTATED   12  0   3   3  0   1   1   0  1  1
  3Q GAIN WILD-TYPE 83  2   4  13  1   3  10   5 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             1       2        2        2        3         1
  3Q GAIN WILD-TYPE           3      15        8       12       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q GAIN MUTATED           0         1         0          2          4
  3Q GAIN WILD-TYPE        10         7         9          4         14
                   vv
clus                STAGE IIIC STAGE IV
  3Q GAIN MUTATED            3        0
  3Q GAIN WILD-TYPE         20        6
D6V8, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    7  3
  4P GAIN WILD-TYPE 37 47
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10                84 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                47 
$`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-FS-A4F2 TCGA-GN-A264 TCGA-GN-A26D 
        5.95         3.22        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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        24.00         9.30         5.39         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        2.86        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.96        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.47         8.12         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         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-A3PL TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       42.84        78.44         1.71        72.16         8.81        53.82 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        15.35 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        84.72        10.09        16.21        15.39        12.16 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             3.22              0.13 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            48.79             98.76 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            14.01             11.23 
[1] "3.2 - 48.8 (14.0)" "0.1 - 98.8 (11.2)"
       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-A2JF        TCGA-D3-A2JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
[1] "hr=" "2.1"
D7V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P GAIN MUTATED                    3             0
  4P GAIN WILD-TYPE                 22             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P GAIN MUTATED                                                                                          4
  4P GAIN WILD-TYPE                                                                                       31
                   vv
clus                REGIONAL LYMPH NODE
  4P GAIN MUTATED                    10
  4P GAIN WILD-TYPE                 102
D7V3, multiclass
                                                                                          clus
vv                                                                                         4P GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            1
  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      8    9
  4P GAIN WILD-TYPE   59   97
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               8                59
  MALE                 9                97
                   vv
clus                 M0  M1 M1A M1B M1C
  4P GAIN MUTATED    15   0   0   0   0
  4P GAIN WILD-TYPE 135   2   2   2   2
D7V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P GAIN MUTATED    8  0   3   1  0   0   1   1  2  0
  4P GAIN WILD-TYPE 87  2   4  15  1   4  10   4 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        1         0
  4P GAIN WILD-TYPE           4      16        9       13       18         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P GAIN MUTATED           0         4         2          2          2
  4P GAIN WILD-TYPE        10         4         7          4         16
                   vv
clus                STAGE IIIC STAGE IV
  4P GAIN MUTATED            2        0
  4P GAIN WILD-TYPE         21        6
D7V8, multiclass

Clustering(8) Variable = 4q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    6  3
  4Q GAIN WILD-TYPE 38 47
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9                85 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                47 
$`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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        24.00         9.30         5.39         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        2.86        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.96        37.97        38.63         4.41         1.08        27.12 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
        9.47         8.12         8.84         9.99         6.48         2.43 
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-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       78.44         6.58         1.71        72.16         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 
       15.35        24.85        84.72        10.09        16.21        15.39 
TCGA-GN-A26A 
       12.16 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             5.95              0.13 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            48.79             98.76 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            14.70             11.11 
[1] "6.0 - 48.8 (14.7)" "0.1 - 98.8 (11.1)"
       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-A2JF        TCGA-D3-A2JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q GAIN WILD-TYPE"   "4Q GAIN MUTATED" 
[1] "hr=" "2.2"
D8V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q GAIN MUTATED                    1             0
  4Q GAIN WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q GAIN MUTATED                                                                                          2
  4Q GAIN WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  4Q GAIN MUTATED                    10
  4Q GAIN WILD-TYPE                 102
D8V3, multiclass
                                                                                          clus
vv                                                                                         4Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  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      5    8
  4Q GAIN WILD-TYPE   62   98
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               5                62
  MALE                 8                98
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q GAIN MUTATED    10   0   0   0   0
  4Q GAIN WILD-TYPE 140   2   2   2   2
D8V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q GAIN MUTATED    4  0   2   2  0   0   1   0  2  0
  4Q GAIN WILD-TYPE 91  2   5  14  1   4  10   5 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           4      17       10       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q GAIN MUTATED           0         3         1          1          2
  4Q GAIN WILD-TYPE        10         5         8          5         16
                   vv
clus                STAGE IIIC STAGE IV
  4Q GAIN MUTATED            3        0
  4Q GAIN WILD-TYPE         20        6
D8V8, multiclass

Clustering(9) Variable = 5p gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    5  4
  5P GAIN WILD-TYPE 39 46
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                9                85 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                46 
$`5P GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A2JF TCGA-DA-A1HV TCGA-EE-A20H TCGA-EE-A29T TCGA-EE-A2A0 
       32.55        30.87        48.79         8.81         6.48        11.31 
TCGA-ER-A19M TCGA-FW-A3I3 TCGA-FW-A3TU 
       28.64         0.20         0.13 

$`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-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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.96        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
        3.22        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 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.13              1.02 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            48.79             98.76 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            11.31             11.57 
[1] "0.1 - 48.8 (11.3)" "1.0 - 98.8 (11.6)"
       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-A2JF        TCGA-D3-A2JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       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-A4F2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       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-A4F2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       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-A4F2 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P GAIN MUTATED                    6             0
  5P GAIN WILD-TYPE                 19             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P GAIN MUTATED                                                                                          1
  5P GAIN WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  5P GAIN MUTATED                    12
  5P GAIN WILD-TYPE                 100
D9V3, multiclass
                                                                                          clus
vv                                                                                         5P GAIN MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         5P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      19
  PRIMARY TUMOR                                                                                            1
  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      8   11
  5P GAIN WILD-TYPE   59   95
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               8                59
  MALE                11                95
                   vv
clus                 M0  M1 M1A M1B M1C
  5P GAIN MUTATED    16   1   0   1   0
  5P GAIN WILD-TYPE 134   1   2   1   2
D9V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P GAIN MUTATED   13  0   0   1  0   1   1   0  1  1
  5P GAIN WILD-TYPE 82  2   7  15  1   3  10   5 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       3        2        1        2         1
  5P GAIN WILD-TYPE           3      14        8       13       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P GAIN MUTATED           0         2         0          0          2
  5P GAIN WILD-TYPE        10         6         9          6         16
                   vv
clus                STAGE IIIC STAGE IV
  5P GAIN MUTATED            0        1
  5P GAIN WILD-TYPE         23        5
D9V8, multiclass

Clustering(10) Variable = 5q gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    2  0
  5Q GAIN WILD-TYPE 42 50
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                92 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                50 
$`5Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-FW-A3TU 
       30.87         0.13 

$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 
        3.22        10.78         6.41         0.20         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 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.13              0.20 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            30.87             98.76 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            15.50             11.49 
[1] "0.1 - 30.9 (15.5)" "0.2 - 98.8 (11.5)"
       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-A2JF        TCGA-D3-A2JK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                92 
       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-A1I5        TCGA-DA-A1I7 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB        TCGA-DA-A1IC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A182 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B        TCGA-EE-A20F 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29M 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V        TCGA-EE-A29X 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A44A 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2        TCGA-FS-A4F9 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-GN-A261 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D10V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q GAIN MUTATED                    3             0
  5Q GAIN WILD-TYPE                 22             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q GAIN MUTATED                                                                                          0
  5Q GAIN WILD-TYPE                                                                                       35
                   vv
clus                REGIONAL LYMPH NODE
  5Q GAIN MUTATED                     4
  5Q GAIN WILD-TYPE                 108
D10V3, multiclass
                                                                                          clus
vv                                                                                         5Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    4
                                                                                          clus
vv                                                                                         5Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    108
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2    5
  5Q GAIN WILD-TYPE   65  101
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               2                65
  MALE                 5               101
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q GAIN MUTATED     6   0   0   0   0
  5Q GAIN WILD-TYPE 144   2   2   2   2
D10V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q GAIN MUTATED    5  0   0   0  0   1   0   0  0  0
  5Q GAIN WILD-TYPE 90  2   7  16  1   3  11   5 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        2         1
  5Q GAIN WILD-TYPE           4      16        9       14       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q GAIN MUTATED           0         0         0          0          0
  5Q GAIN WILD-TYPE        10         8         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  5Q GAIN MUTATED            0        0
  5Q GAIN WILD-TYPE         23        6
D10V8, multiclass

Clustering(11) Variable = 6p gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   10 17
  6P GAIN WILD-TYPE 34 33
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               27                67 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               17                33 
$`6P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q7 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A3C6 TCGA-DA-A1HV 
       16.47        98.76        21.14        30.87        15.25        48.79 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EE-A17Z TCGA-EE-A181 
       10.03        13.68         4.93         7.00         6.31         1.12 
TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2A5 
        4.27         8.81        12.03         8.84         9.99         9.67 
TCGA-ER-A19M TCGA-ER-A19N TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 
       28.64        42.84         3.22         0.20         0.13        31.33 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A26D 
       10.09        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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 
       19.36        17.56        14.83        11.57         1.35        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
       36.07         5.13         7.96        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
        4.41         1.08        27.12         9.47         8.12         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
        2.43         8.09        11.31        25.28        23.90         8.94 
TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET 
        3.52        11.11         4.18        12.99        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-A267 
        6.41         1.02        15.35        24.85        84.72        16.21 
TCGA-GN-A268 
       15.39 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.13              1.02 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            98.76             84.72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            10.09             11.57 
[1] "0.1 - 98.8 (10.1)" "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-A2JF        TCGA-D3-A2JK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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-A4F2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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-A4F2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "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-A4F2 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6P GAIN MUTATED"   "6P GAIN MUTATED" 
[1] "hr=" "1.5"
D11V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P GAIN MUTATED                   14             0
  6P GAIN WILD-TYPE                 11             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P GAIN MUTATED                                                                                          9
  6P GAIN WILD-TYPE                                                                                       26
                   vv
clus                REGIONAL LYMPH NODE
  6P GAIN MUTATED                    35
  6P GAIN WILD-TYPE                  77
D11V3, multiclass
                                                                                          clus
vv                                                                                         6P GAIN MUTATED
  DISTANT METASTASIS                                                                                    14
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               9
  REGIONAL LYMPH NODE                                                                                   35
                                                                                          clus
vv                                                                                         6P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      11
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                26
  REGIONAL LYMPH NODE                                                                                     77
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     27   31
  6P GAIN WILD-TYPE   40   75
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              27                40
  MALE                31                75
                   vv
clus                 M0  M1 M1A M1B M1C
  6P GAIN MUTATED    48   1   1   0   0
  6P GAIN WILD-TYPE 102   1   1   2   2
D11V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P GAIN MUTATED   35  0   3   4  0   2   3   0  4  0
  6P GAIN WILD-TYPE 60  2   4  12  1   2   8   5 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             1       5        4        5        6         3
  6P GAIN WILD-TYPE           3      12        6        9       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P GAIN MUTATED           5         5         0          3          5
  6P GAIN WILD-TYPE         5         3         9          3         13
                   vv
clus                STAGE IIIC STAGE IV
  6P GAIN MUTATED            6        1
  6P GAIN WILD-TYPE         17        5
D11V8, multiclass

Clustering(12) Variable = 6q gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    3  3
  6Q GAIN WILD-TYPE 41 47
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                88 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                47 
$`6Q GAIN MUTATED`
TCGA-D3-A1Q7 TCGA-DA-A1I0 TCGA-EE-A29R TCGA-ER-A19M TCGA-FS-A4F2 TCGA-FW-A3TU 
       98.76        10.03         8.84        28.64         3.22         0.13 

$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I1 TCGA-DA-A1I2 
        2.86        48.79        35.80        51.12        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        5.13         8.81         7.96        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
        4.41         1.08        27.12         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       12.99        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-A3I3 
       72.16         8.81        53.82        10.78         6.41         0.20 
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 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.13              0.20 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            98.76             84.72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            9.435            11.800 
[1] "0.1 - 98.8 (9.4)"  "0.2 - 84.7 (11.8)"
       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-A2JF        TCGA-D3-A2JK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4F2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4F2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "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-A4F2 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D12V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q GAIN MUTATED                    3             0
  6Q GAIN WILD-TYPE                 22             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q GAIN MUTATED                                                                                          2
  6Q GAIN WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  6Q GAIN MUTATED                     7
  6Q GAIN WILD-TYPE                 105
D12V3, multiclass
                                                                                          clus
vv                                                                                         6Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    7
                                                                                          clus
vv                                                                                         6Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            1
  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      6    6
  6Q GAIN WILD-TYPE   61  100
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               6                61
  MALE                 6               100
                   vv
clus                 M0  M1 M1A M1B M1C
  6Q GAIN MUTATED    10   0   1   0   0
  6Q GAIN WILD-TYPE 140   2   1   2   2
D12V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q GAIN MUTATED    8  0   0   2  0   0   0   0  1  0
  6Q GAIN WILD-TYPE 87  2   7  14  1   4  11   5 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        2         1
  6Q GAIN WILD-TYPE           4      17       10       11       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q GAIN MUTATED           1         1         0          0          0
  6Q GAIN WILD-TYPE         9         7         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  6Q GAIN MUTATED            2        0
  6Q GAIN WILD-TYPE         21        6
D12V8, multiclass

Clustering(13) Variable = 7p gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   14 25
  7P GAIN WILD-TYPE 30 25
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               39                55 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                25 
$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A181 
       44.52        36.69        25.15         4.93         6.64         1.12 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N 
        8.81         7.96        37.97        11.15        38.63         9.47 
TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A0 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A3PL 
       12.03         6.48        11.31         8.94         4.18         1.71 
TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A266 
        5.95         8.81         3.22         0.20        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-A2JF 
       98.76        28.08        10.26         8.38        21.14        30.87 
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-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
        4.01        35.80        39.19        22.36        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        4.27        36.07         5.13         4.41         1.08        27.12 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 
        8.12         8.84         9.99         2.43         8.09        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M 
       23.90         9.67         3.52        11.11        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 
       42.84        78.44         6.58        72.16        53.82        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 
        6.41         1.02         0.13        15.35        24.85        84.72 
TCGA-GN-A268 
       15.39 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.20              0.13 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            70.16             98.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            11.15             12.99 
[1] "0.2 - 70.2 (11.2)" "0.1 - 98.8 (13.0)"
       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-A2JF        TCGA-D3-A2JK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4F2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4F2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       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-A4F2 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" 
[1] "hr=" "1.5"
D13V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P GAIN MUTATED                   10             0
  7P GAIN WILD-TYPE                 15             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P GAIN MUTATED                                                                                         19
  7P GAIN WILD-TYPE                                                                                       16
                   vv
clus                REGIONAL LYMPH NODE
  7P GAIN MUTATED                    44
  7P GAIN WILD-TYPE                  68
D13V3, multiclass
                                                                                          clus
vv                                                                                         7P GAIN MUTATED
  DISTANT METASTASIS                                                                                    10
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              19
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      15
  PRIMARY TUMOR                                                                                            1
  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     25   48
  7P GAIN WILD-TYPE   42   58
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              25                42
  MALE                48                58
                   vv
clus                M0 M1 M1A M1B M1C
  7P GAIN MUTATED   60  2   2   0   2
  7P GAIN WILD-TYPE 90  0   0   2   0
D13V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7P GAIN MUTATED   36  0   5   9  0   2   4   4  5  2
  7P GAIN WILD-TYPE 59  2   2   7  1   2   7   1 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             2       6        5        2        8         3
  7P GAIN WILD-TYPE           2      11        5       12       11         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P GAIN MUTATED           2         4         3          5         10
  7P GAIN WILD-TYPE         8         4         6          1          8
                   vv
clus                STAGE IIIC STAGE IV
  7P GAIN MUTATED            8        5
  7P GAIN WILD-TYPE         15        1
D13V8, multiclass

Clustering(14) Variable = 7q gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   17 24
  7Q GAIN WILD-TYPE 27 26
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               41                53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               24                26 
$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC 
        9.99        44.52        36.69        25.15         4.93         6.64 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29A 
       17.56        14.83         1.12        12.20         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29T TCGA-EE-A2A0 
       37.97        38.63         9.47        12.03         6.48        11.31 
TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-FS-A4F2 
        8.94         4.18         1.71         5.95         8.81         3.22 
TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        0.20        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-A2JF 
       98.76        28.08        10.26         8.38        21.14        30.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 
        6.35        15.25        45.70        13.32        24.00         4.01 
TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-EE-A17X 
       35.80        39.19        22.36        19.36         7.00        11.57 
TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29D 
        6.31         1.35         4.27        36.07         5.13        11.15 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41         1.08        27.12         8.12         8.84         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        2.43         8.09        25.28        23.90         9.67         3.52 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.11        12.99        28.64        42.84        78.44         6.58 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU 
       72.16        53.82        10.78         6.41         1.02         0.13 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A268 
       15.35        24.85        84.72        10.09        15.39 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.20              0.13 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.16             98.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            11.41             11.57 
[1] "0.2 - 70.2 (11.4)" "0.1 - 98.8 (11.6)"
       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-A2JF        TCGA-D3-A2JK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4F2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4F2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       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-A4F2 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
[1] "hr=" "1.3"
D14V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q GAIN MUTATED                   12             0
  7Q GAIN WILD-TYPE                 13             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q GAIN MUTATED                                                                                         18
  7Q GAIN WILD-TYPE                                                                                       17
                   vv
clus                REGIONAL LYMPH NODE
  7Q GAIN MUTATED                    44
  7Q GAIN WILD-TYPE                  68
D14V3, multiclass
                                                                                          clus
vv                                                                                         7Q GAIN MUTATED
  DISTANT METASTASIS                                                                                    12
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              18
  REGIONAL LYMPH NODE                                                                                   44
                                                                                          clus
vv                                                                                         7Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      13
  PRIMARY TUMOR                                                                                            1
  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     28   46
  7Q GAIN WILD-TYPE   39   60
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              28                39
  MALE                46                60
                   vv
clus                M0 M1 M1A M1B M1C
  7Q GAIN MUTATED   63  2   2   0   2
  7Q GAIN WILD-TYPE 87  0   0   2   0
D14V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7Q GAIN MUTATED   37  0   5   8  0   3   5   4  6  2
  7Q GAIN WILD-TYPE 58  2   2   8  1   1   6   1 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             3       6        4        2        9         2
  7Q GAIN WILD-TYPE           1      11        6       12       10         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q GAIN MUTATED           2         5         3          5         12
  7Q GAIN WILD-TYPE         8         3         6          1          6
                   vv
clus                STAGE IIIC STAGE IV
  7Q GAIN MUTATED            8        5
  7Q GAIN WILD-TYPE         15        1
D14V8, multiclass

Clustering(15) Variable = 8p gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   11 12
  8P GAIN WILD-TYPE 33 38
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               23                71 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                38 
$`8P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A2JF TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1HY 
       70.16        30.87        45.70        13.32         5.39        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29E 
       39.19        13.68         9.99        17.56         1.12        38.63 
TCGA-EE-A29R TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N TCGA-FS-A1ZR 
        8.84         4.18        12.99        28.64        42.84         8.81 
TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
        3.22         0.20        16.21        12.16        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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 
       19.36         7.00        14.83        11.57         6.31         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       12.20         4.27        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
       12.03         8.12         9.99         6.48         2.43         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-FW-A3TU TCGA-GN-A261 
       53.82        10.78         6.41         1.02         0.13        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 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.20              0.13 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.16             98.76 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            13.68             11.11 
[1] "0.2 - 70.2 (13.7)" "0.1 - 98.8 (11.1)"
       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-A2JF        TCGA-D3-A2JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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-A4F2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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-A4F2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8P GAIN MUTATED"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "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-A4F2 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" 
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P GAIN MUTATED                    5             0
  8P GAIN WILD-TYPE                 20             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P GAIN MUTATED                                                                                         11
  8P GAIN WILD-TYPE                                                                                       24
                   vv
clus                REGIONAL LYMPH NODE
  8P GAIN MUTATED                    19
  8P GAIN WILD-TYPE                  93
D15V3, multiclass
                                                                                          clus
vv                                                                                         8P GAIN MUTATED
  DISTANT METASTASIS                                                                                     5
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              11
  REGIONAL LYMPH NODE                                                                                   19
                                                                                          clus
vv                                                                                         8P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      20
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                24
  REGIONAL LYMPH NODE                                                                                     93
D15V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     11   24
  8P GAIN WILD-TYPE   56   82
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              11                56
  MALE                24                82
                   vv
clus                 M0  M1 M1A M1B M1C
  8P GAIN MUTATED    29   2   0   0   0
  8P GAIN WILD-TYPE 121   0   2   2   2
D15V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P GAIN MUTATED   17  0   3   5  0   1   2   0  4  0
  8P GAIN WILD-TYPE 78  2   4  11  1   3   9   5 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        1        2        5         2
  8P GAIN WILD-TYPE           4      16        9       12       14         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P GAIN MUTATED           1         4         2          2          4
  8P GAIN WILD-TYPE         9         4         7          4         14
                   vv
clus                STAGE IIIC STAGE IV
  8P GAIN MUTATED            6        2
  8P GAIN WILD-TYPE         17        4
D15V8, multiclass

Clustering(16) Variable = 8q gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   13 20
  8Q GAIN WILD-TYPE 31 30
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               33                61 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               20                30 
$`8Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A3CC 
       16.47        70.16        22.55        10.26        30.87        45.70 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 
       13.32         9.30         5.39        51.12        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17Z TCGA-EE-A181 
       13.68         9.99         7.00        17.56         6.31         1.12 
TCGA-EE-A29E TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A5 TCGA-ER-A19J TCGA-ER-A19L 
       38.63         8.84         6.48         9.67         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A3ET TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FW-A3I3 
       28.64        42.84         6.58         8.81         3.22         0.20 
TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       35.80        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A183 
        6.64        19.36        14.83        11.57         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        4.27        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.12         9.99         2.43         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A1A1 TCGA-ER-A3PL 
       23.90         8.94         3.52        11.11        78.44         1.71 
TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
        5.95        72.16        53.82        10.78         6.41         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A268 
       15.39 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.20              0.13 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            70.16             98.76 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            12.16             11.41 
[1] "0.2 - 70.2 (12.2)" "0.1 - 98.8 (11.4)"
       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-A2JF        TCGA-D3-A2JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A4F2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A4F2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       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-A4F2 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
[1] "hr=" "1.3"
D16V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q GAIN MUTATED                    8             0
  8Q GAIN WILD-TYPE                 17             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q GAIN MUTATED                                                                                         15
  8Q GAIN WILD-TYPE                                                                                       20
                   vv
clus                REGIONAL LYMPH NODE
  8Q GAIN MUTATED                    31
  8Q GAIN WILD-TYPE                  81
D16V3, multiclass
                                                                                          clus
vv                                                                                         8Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     8
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              15
  REGIONAL LYMPH NODE                                                                                   31
                                                                                          clus
vv                                                                                         8Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      17
  PRIMARY TUMOR                                                                                            1
  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     18   36
  8Q GAIN WILD-TYPE   49   70
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              18                49
  MALE                36                70
                   vv
clus                 M0  M1 M1A M1B M1C
  8Q GAIN MUTATED    46   2   1   0   0
  8Q GAIN WILD-TYPE 104   0   1   2   2
D16V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q GAIN MUTATED   27  0   4   5  0   3   3   1  6  1
  8Q GAIN WILD-TYPE 68  2   3  11  1   1   8   4 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        2        4        6         3
  8Q GAIN WILD-TYPE           4      14        8       10       13         5
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q GAIN MUTATED           3         5         3          3          6
  8Q GAIN WILD-TYPE         7         3         6          3         12
                   vv
clus                STAGE IIIC STAGE IV
  8Q GAIN MUTATED            8        2
  8Q GAIN WILD-TYPE         15        4
D16V8, multiclass

Clustering(17) Variable = 9p gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    1  1
  9P GAIN WILD-TYPE 43 49
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                92 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                49 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         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-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             6.58              0.13 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            22.55             98.76 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           14.565            11.490 
[1] "6.6 - 22.6 (14.6)" "0.1 - 98.8 (11.5)"
       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-A2JF        TCGA-D3-A2JK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                92 
       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-A2JF        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-A1I5        TCGA-DA-A1I7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB        TCGA-DA-A1IC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A182 
"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-A20H        TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29M 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V        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-A4F2        TCGA-FS-A4F9        TCGA-FS-A4FC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TU        TCGA-GN-A261 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D17V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P GAIN MUTATED                    0             0
  9P GAIN WILD-TYPE                 25             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P GAIN MUTATED                                                                                          1
  9P GAIN WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  9P GAIN MUTATED                     2
  9P GAIN WILD-TYPE                 110
D17V3, multiclass
                                                                                          clus
vv                                                                                         9P GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         9P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                            1
  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   65  105
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                65
  MALE                 1               105
                   vv
clus                 M0  M1 M1A M1B M1C
  9P GAIN MUTATED     3   0   0   0   0
  9P GAIN WILD-TYPE 147   2   2   2   2
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 94  2   6  16  1   3  11   5 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           4      16       10       14       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P GAIN MUTATED           0         0         0          1          1
  9P GAIN WILD-TYPE        10         8         9          5         17
                   vv
clus                STAGE IIIC STAGE IV
  9P GAIN MUTATED            0        0
  9P GAIN WILD-TYPE         23        6
D17V8, multiclass

Clustering(18) Variable = 9q gain mutation analysis
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    1  1
  9Q GAIN WILD-TYPE 43 49
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                92 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                49 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         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-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
        6.58         1.71         5.95         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            22.55              0.13 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            72.16             98.76 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           47.355            11.360 
[1] "22.6 - 72.2 (47.4)" "0.1 - 98.8 (11.4)" 
       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-A2JF        TCGA-D3-A2JK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        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-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29M        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-A29V 
"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-A4F2 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                92 
       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-A2JF        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-A1I5        TCGA-DA-A1I7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB        TCGA-DA-A1IC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A182 
"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-A20H        TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29M 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V        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-A4F2        TCGA-FS-A4F9        TCGA-FS-A4FC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TU        TCGA-GN-A261 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D18V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q GAIN MUTATED                    0             0
  9Q GAIN WILD-TYPE                 25             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q GAIN MUTATED                                                                                          0
  9Q GAIN WILD-TYPE                                                                                       35
                   vv
clus                REGIONAL LYMPH NODE
  9Q GAIN MUTATED                     3
  9Q GAIN WILD-TYPE                 109
D18V3, multiclass
                                                                                          clus
vv                                                                                         9Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         9Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                            1
  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   65  105
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                65
  MALE                 1               105
                   vv
clus                 M0  M1 M1A M1B M1C
  9Q GAIN MUTATED     3   0   0   0   0
  9Q GAIN WILD-TYPE 147   2   2   2   2
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 93  2   7  16  1   3  11   5 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           4      16       10       14       18         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q GAIN MUTATED           0         0         0          0          1
  9Q GAIN WILD-TYPE        10         8         9          6         17
                   vv
clus                STAGE IIIC STAGE IV
  9Q GAIN MUTATED            0        0
  9Q GAIN WILD-TYPE         23        6
D18V8, multiclass

Clustering(19) Variable = 11p gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    3  3
  11P GAIN WILD-TYPE 41 47
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                 88 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 47 
$`11P GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-EE-A29T TCGA-ER-A19N TCGA-FS-A4F2 
       30.87        13.32         7.00         6.48        42.84         3.22 

$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         2.43         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-A3I3 TCGA-FW-A3R5 
        8.81        53.82        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3.22               0.13 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             42.84              98.76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             10.16              11.49 
[1] "3.2 - 42.8 (10.2)" "0.1 - 98.8 (11.5)"
        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-A2JF         TCGA-D3-A2JK 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE"   "11P GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P GAIN WILD-TYPE"   "11P GAIN MUTATED" "11P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"11P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P GAIN MUTATED                    2             0
  11P GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P GAIN MUTATED                                                                                          1
  11P GAIN WILD-TYPE                                                                                       34
                    vv
clus                 REGIONAL LYMPH NODE
  11P GAIN MUTATED                     8
  11P GAIN WILD-TYPE                 104
D19V3, multiclass
                                                                                          clus
vv                                                                                         11P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         11P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  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      3    8
  11P GAIN WILD-TYPE   64   98
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 64
  MALE                  8                 98
                    vv
clus                  M0  M1 M1A M1B M1C
  11P GAIN MUTATED    10   0   0   0   0
  11P GAIN WILD-TYPE 140   2   2   2   2
D19V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P GAIN MUTATED    5  0   2   1  0   0   1   0  0  1
  11P GAIN WILD-TYPE 90  2   5  15  1   4  10   5 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        1        0        1         1
  11P GAIN WILD-TYPE           4      16        9       14       18         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P GAIN MUTATED           0         1         1          1          2
  11P GAIN WILD-TYPE        10         7         8          5         16
                    vv
clus                 STAGE IIIC STAGE IV
  11P GAIN MUTATED            0        0
  11P GAIN WILD-TYPE         23        6
D19V8, multiclass

Clustering(20) Variable = 11q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    2  3
  11Q GAIN WILD-TYPE 42 47
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 89 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 47 
$`11Q GAIN MUTATED`
TCGA-D3-A2JF TCGA-D3-A3CE TCGA-DA-A3F3 TCGA-ER-A19N TCGA-FS-A4F2 
       30.87        13.32         7.00        42.84         3.22 

$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-A1A1 TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN 
       12.99        28.64        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-A3I3 
       72.16         8.81        53.82        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        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 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3.22               0.13 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             42.84              98.76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             13.32              11.41 
[1] "3.2 - 42.8 (13.3)" "0.1 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q GAIN WILD-TYPE"   "11Q GAIN MUTATED" "11Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"11Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q GAIN MUTATED                    2             0
  11Q GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q GAIN MUTATED                                                                                          1
  11Q GAIN WILD-TYPE                                                                                       34
                    vv
clus                 REGIONAL LYMPH NODE
  11Q GAIN MUTATED                     5
  11Q GAIN WILD-TYPE                 107
D20V3, multiclass
                                                                                          clus
vv                                                                                         11Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         11Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  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      2    6
  11Q GAIN WILD-TYPE   65  100
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                2                 65
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q GAIN MUTATED     7   0   0   0   0
  11Q GAIN WILD-TYPE 143   2   2   2   2
D20V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q GAIN MUTATED    4  0   1   1  0   0   1   0  0  0
  11Q GAIN WILD-TYPE 91  2   6  15  1   4  10   5 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        1        0        1         1
  11Q GAIN WILD-TYPE           4      17        9       14       18         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q GAIN MUTATED           0         1         1          0          2
  11Q GAIN WILD-TYPE        10         7         8          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  11Q GAIN MUTATED            0        0
  11Q GAIN WILD-TYPE         23        6
D20V8, multiclass

Clustering(21) Variable = 12p gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5 10
  12P GAIN WILD-TYPE 39 40
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                15                 79 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                10                 40 
$`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-A1IA TCGA-DA-A3F5 TCGA-EE-A20H TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L 
        4.93        17.56         8.81         8.94         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A3PL TCGA-GN-A26A 
       28.64         1.71        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF 
       11.41        30.87         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-A1I5 TCGA-DA-A1I8 
       10.03        39.19        13.68         9.99        44.52        25.15 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X 
       22.36         6.64        19.36         7.00        14.83        11.57 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        5.13         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-A4F2 
        6.58         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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-A26D 
       14.70 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.71               0.13 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             70.16              98.76 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             12.99              11.31 
[1] "1.7 - 70.2 (13.0)" "0.1 - 98.8 (11.3)"
        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-A2JF         TCGA-D3-A2JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "12P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "12P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "12P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "12P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "12P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "12P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12P GAIN MUTATED"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-GN-A26D 
"12P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D21V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P GAIN MUTATED                    3             0
  12P GAIN WILD-TYPE                 22             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P GAIN MUTATED                                                                                          6
  12P GAIN WILD-TYPE                                                                                       29
                    vv
clus                 REGIONAL LYMPH NODE
  12P GAIN MUTATED                    10
  12P GAIN WILD-TYPE                 102
D21V3, multiclass
                                                                                          clus
vv                                                                                         12P GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    10
                                                                                          clus
vv                                                                                         12P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                             1
  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      6   13
  12P GAIN WILD-TYPE   61   93
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                6                 61
  MALE                 13                 93
                    vv
clus                  M0  M1 M1A M1B M1C
  12P GAIN MUTATED    16   1   1   0   0
  12P GAIN WILD-TYPE 134   1   1   2   2
D21V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P GAIN MUTATED    6  0   2   3  0   2   1   1  3  0
  12P GAIN WILD-TYPE 89  2   5  13  1   2  10   4 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       2        1        1        0         0
  12P GAIN WILD-TYPE           4      15        9       13       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P GAIN MUTATED           0         1         3          2          4
  12P GAIN WILD-TYPE        10         7         6          4         14
                    vv
clus                 STAGE IIIC STAGE IV
  12P GAIN MUTATED            2        2
  12P GAIN WILD-TYPE         21        4
D21V8, multiclass

Clustering(22) Variable = 12q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    1  4
  12Q GAIN WILD-TYPE 43 46
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 5                 89 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 46 
$`12Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A1Q9 TCGA-DA-A3F5 TCGA-ER-A19L TCGA-GN-A26A 
       70.16        22.55        17.56        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
        6.64        19.36         7.00        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       72.16         8.81        53.82         3.22        10.78         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
        0.20         1.02         0.13        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 
             12.16               0.13 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             70.16              98.76 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             17.56              11.15 
[1] "12.2 - 70.2 (17.6)" "0.1 - 98.8 (11.2)" 
        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-A2JF         TCGA-D3-A2JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-GN-A26D 
"12Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q GAIN MUTATED                    1             0
  12Q GAIN WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q GAIN MUTATED                                                                                          2
  12Q GAIN WILD-TYPE                                                                                       33
                    vv
clus                 REGIONAL LYMPH NODE
  12Q GAIN MUTATED                     4
  12Q GAIN WILD-TYPE                 108
D22V3, multiclass
                                                                                          clus
vv                                                                                         12Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     4
                                                                                          clus
vv                                                                                         12Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     108
D22V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    6
  12Q GAIN WILD-TYPE   66  100
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 66
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q GAIN MUTATED     6   0   0   0   0
  12Q GAIN WILD-TYPE 144   2   2   2   2
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 94  2   5  15  1   3  11   5 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        0        0        1         0
  12Q GAIN WILD-TYPE           4      17       10       14       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q GAIN MUTATED           0         0         1          2          1
  12Q GAIN WILD-TYPE        10         8         8          4         17
                    vv
clus                 STAGE IIIC STAGE IV
  12Q GAIN MUTATED            1        0
  12Q GAIN WILD-TYPE         22        6
D22V8, multiclass

Clustering(23) Variable = 13q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    7 11
  13Q GAIN WILD-TYPE 37 39
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                 76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                11                 39 
$`13Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2JF TCGA-D3-A3CE TCGA-DA-A1I7 TCGA-DA-A3F3 TCGA-EE-A20H 
       16.47        30.87        13.32        36.69         7.00         8.81 
TCGA-EE-A29A TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19L TCGA-ER-A19M 
        7.96        12.03         8.84         9.67        12.99        28.64 
TCGA-ER-A19N TCGA-ER-A3PL TCGA-FS-A4F2 TCGA-FW-A3TU TCGA-GN-A267 TCGA-GN-A268 
       42.84         1.71         3.22         0.13        16.21        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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
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-A29M TCGA-EE-A29N TCGA-EE-A29Q 
       38.63         4.41         1.08        27.12         9.47         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         8.09        11.31        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A1A1 
       23.90         8.94         3.52        11.11         4.18        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-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
        6.41         0.20         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 
              0.13               0.20 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             42.84              98.76 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.51              11.36 
[1] "0.1 - 42.8 (12.5)" "0.2 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED"   "13Q GAIN MUTATED" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"13Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q GAIN MUTATED                   10             0
  13Q GAIN WILD-TYPE                 15             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q GAIN MUTATED                                                                                          6
  13Q GAIN WILD-TYPE                                                                                       29
                    vv
clus                 REGIONAL LYMPH NODE
  13Q GAIN MUTATED                    14
  13Q GAIN WILD-TYPE                  98
D23V3, multiclass
                                                                                          clus
vv                                                                                         13Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     10
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    14
                                                                                          clus
vv                                                                                         13Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       15
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      98
D23V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     11   19
  13Q GAIN WILD-TYPE   56   87
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               11                 56
  MALE                 19                 87
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q GAIN MUTATED    24   0   1   0   0
  13Q GAIN WILD-TYPE 126   2   1   2   2
D23V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q GAIN MUTATED   14  0   4   4  0   0   2   0  1  0
  13Q GAIN WILD-TYPE 81  2   3  12  1   4   9   5 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        2        3        0         1
  13Q GAIN WILD-TYPE           4      16        8       11       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q GAIN MUTATED           2         4         2          3          3
  13Q GAIN WILD-TYPE         8         4         7          3         15
                    vv
clus                 STAGE IIIC STAGE IV
  13Q GAIN MUTATED            3        1
  13Q GAIN WILD-TYPE         20        5
D23V8, multiclass

Clustering(24) Variable = 14q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    2  6
  14Q GAIN WILD-TYPE 42 44
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                 86 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                 44 
$`14Q GAIN MUTATED`
TCGA-D3-A1Q9 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A20H TCGA-EE-A29L TCGA-ER-A19L 
       22.55        13.68        36.69         8.81         1.08        12.99 
TCGA-ER-A19M TCGA-GN-A26D 
       28.64        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M 
        7.96        37.97        11.15        38.63         4.41        27.12 
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-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
        8.94         3.52        11.11         4.18        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
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 
       15.39        12.16 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.08               0.13 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             36.69              98.76 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             14.19              11.23 
[1] "1.1 - 36.7 (14.2)" "0.1 - 98.8 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "14Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "14Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"14Q GAIN WILD-TYPE"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "14Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "14Q GAIN MUTATED"   "14Q GAIN MUTATED" "14Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "14Q GAIN MUTATED" 
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q GAIN MUTATED                    2             0
  14Q GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q GAIN MUTATED                                                                                          3
  14Q GAIN WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  14Q GAIN MUTATED                     9
  14Q GAIN WILD-TYPE                 103
D24V3, multiclass
                                                                                          clus
vv                                                                                         14Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         14Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  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   10
  14Q GAIN WILD-TYPE   63   96
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                4                 63
  MALE                 10                 96
                    vv
clus                  M0  M1 M1A M1B M1C
  14Q GAIN MUTATED    12   0   0   0   0
  14Q GAIN WILD-TYPE 138   2   2   2   2
D24V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q GAIN MUTATED    9  0   0   0  0   1   2   0  1  0
  14Q GAIN WILD-TYPE 86  2   7  16  1   3   9   5 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       2        1        1        2         0
  14Q GAIN WILD-TYPE           4      15        9       13       17         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q GAIN MUTATED           1         2         0          0          2
  14Q GAIN WILD-TYPE         9         6         9          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  14Q GAIN MUTATED            2        0
  14Q GAIN WILD-TYPE         21        6
D24V8, multiclass

Clustering(25) Variable = 15q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6 11
  15Q GAIN WILD-TYPE 38 39
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                17                 77 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 39 
$`15Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J9 TCGA-D3-A2JF TCGA-D3-A3CE TCGA-D3-A3MV 
       32.55        22.55        21.14        30.87        13.32         5.39 
TCGA-DA-A1HW TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A183 TCGA-EE-A20H TCGA-EE-A29D 
       35.80        36.69        17.56        12.20         8.81        11.15 
TCGA-EE-A2A1 TCGA-ER-A19M TCGA-FR-A44A TCGA-FS-A4F2 TCGA-GN-A264 
       25.28        28.64        72.16         3.22        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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
        6.64        19.36         7.00        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
        1.12         1.35         4.27        36.07         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 
        0.20         1.02         0.13        15.35        24.85        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3.22               0.13 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             72.16              98.76 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             22.55              10.26 
[1] "3.2 - 72.2 (22.6)" "0.1 - 98.8 (10.3)"
        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-A2JF         TCGA-D3-A2JK 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "15Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "15Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "15Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"15Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q GAIN MUTATED                    5             0
  15Q GAIN WILD-TYPE                 20             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q GAIN MUTATED                                                                                          5
  15Q GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  15Q GAIN MUTATED                    16
  15Q GAIN WILD-TYPE                  96
D25V3, multiclass
                                                                                          clus
vv                                                                                         15Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    16
                                                                                          clus
vv                                                                                         15Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                             1
  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     10   16
  15Q GAIN WILD-TYPE   57   90
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               10                 57
  MALE                 16                 90
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q GAIN MUTATED    24   0   0   0   0
  15Q GAIN WILD-TYPE 126   2   2   2   2
D25V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q GAIN MUTATED   15  0   0   4  0   2   1   0  2  0
  15Q GAIN WILD-TYPE 80  2   7  12  1   2  10   5 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       4        2        2        2         1
  15Q GAIN WILD-TYPE           3      13        8       12       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q GAIN MUTATED           1         2         1          0          4
  15Q GAIN WILD-TYPE         9         6         8          6         14
                    vv
clus                 STAGE IIIC STAGE IV
  15Q GAIN MUTATED            3        0
  15Q GAIN WILD-TYPE         20        6
D25V8, multiclass

Clustering(26) Variable = 16p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  6
  16P GAIN WILD-TYPE 43 44
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 87 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 6                 44 
$`16P GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A29R TCGA-EE-A2A5 TCGA-ER-A19D 
       70.16        13.32         8.81         8.84         9.67         3.52 
TCGA-ER-A19M 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        5.13         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        27.12         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         8.09        11.31        25.28        23.90 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.52               0.13 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             70.16              98.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              9.67              11.57 
[1] "3.5 - 70.2 (9.7)"  "0.1 - 98.8 (11.6)"
        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-A2JF         TCGA-D3-A2JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"16P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P GAIN MUTATED                    2             0
  16P GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P GAIN MUTATED                                                                                          5
  16P GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  16P GAIN MUTATED                     6
  16P GAIN WILD-TYPE                 106
D26V3, multiclass
                                                                                          clus
vv                                                                                         16P GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         16P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     106
D26V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    8
  16P GAIN WILD-TYPE   62   98
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 62
  MALE                  8                 98
                    vv
clus                  M0  M1 M1A M1B M1C
  16P GAIN MUTATED    13   0   0   0   0
  16P GAIN WILD-TYPE 137   2   2   2   2
D26V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P GAIN MUTATED    9  0   1   3  0   0   0   0  0  0
  16P GAIN WILD-TYPE 86  2   6  13  1   4  11   5 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       2        1        3        0         1
  16P GAIN WILD-TYPE           4      15        9       11       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P GAIN MUTATED           1         1         2          1          0
  16P GAIN WILD-TYPE         9         7         7          5         18
                    vv
clus                 STAGE IIIC STAGE IV
  16P GAIN MUTATED            1        0
  16P GAIN WILD-TYPE         22        6
D26V8, multiclass

Clustering(27) Variable = 16q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    1  5
  16Q GAIN WILD-TYPE 43 45
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 88 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 45 
$`16Q GAIN MUTATED`
TCGA-D3-A1Q6 TCGA-D3-A3CE TCGA-EE-A20H TCGA-EE-A29R TCGA-ER-A19D TCGA-ER-A19M 
       70.16        13.32         8.81         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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        5.13         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
        1.08        27.12         9.47        12.03         8.12         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N 
        9.67         8.94        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              3.52               0.13 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             70.16              98.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             11.08              11.49 
[1] "3.5 - 70.2 (11.1)" "0.1 - 98.8 (11.5)"
        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-A2JF         TCGA-D3-A2JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "16Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"16Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q GAIN MUTATED                    2             0
  16Q GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q GAIN MUTATED                                                                                          4
  16Q GAIN WILD-TYPE                                                                                       31
                    vv
clus                 REGIONAL LYMPH NODE
  16Q GAIN MUTATED                     6
  16Q GAIN WILD-TYPE                 106
D27V3, multiclass
                                                                                          clus
vv                                                                                         16Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     6
                                                                                          clus
vv                                                                                         16Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  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    8
  16Q GAIN WILD-TYPE   63   98
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                 63
  MALE                  8                 98
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q GAIN MUTATED    12   0   0   0   0
  16Q GAIN WILD-TYPE 138   2   2   2   2
D27V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q GAIN MUTATED    7  0   1   4  0   0   0   0  0  0
  16Q GAIN WILD-TYPE 88  2   6  12  1   4  11   5 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       2        0        2        0         1
  16Q GAIN WILD-TYPE           4      15       10       12       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q GAIN MUTATED           1         1         2          1          1
  16Q GAIN WILD-TYPE         9         7         7          5         17
                    vv
clus                 STAGE IIIC STAGE IV
  16Q GAIN MUTATED            1        0
  16Q GAIN WILD-TYPE         22        6
D27V8, multiclass

Clustering(28) Variable = 17p gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    7  4
  17P GAIN WILD-TYPE 37 46
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                11                 83 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 46 
$`17P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-EE-A20F 
       16.47        13.32         5.39        36.69         4.93         5.13 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-GN-A26D 
        9.47        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       45.70        24.00         9.30         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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       12.20         4.27        36.07         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
       11.15        38.63         4.41         1.08        27.12         8.12 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        8.84         9.99         6.48         2.43         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       25.28        23.90         9.67         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-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC 
       72.16         8.81        53.82         3.22        10.78         6.41 
TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
        0.20         1.02         0.13        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.71               0.13 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.69              98.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.47              11.57 
[1] "1.7 - 36.7 (9.5)"  "0.1 - 98.8 (11.6)"
        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-A2JF         TCGA-D3-A2JK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17P GAIN MUTATED" "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-A182         TCGA-EE-A183 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "17P GAIN MUTATED" 
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P GAIN MUTATED                    1             0
  17P GAIN WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P GAIN MUTATED                                                                                          5
  17P GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  17P GAIN MUTATED                     8
  17P GAIN WILD-TYPE                 104
D28V3, multiclass
                                                                                          clus
vv                                                                                         17P GAIN MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     8
                                                                                          clus
vv                                                                                         17P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  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      7    7
  17P GAIN WILD-TYPE   60   99
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                7                 60
  MALE                  7                 99
                    vv
clus                  M0  M1 M1A M1B M1C
  17P GAIN MUTATED    11   0   1   0   0
  17P GAIN WILD-TYPE 139   2   1   2   2
D28V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P GAIN MUTATED    8  0   0   2  0   1   1   0  1  0
  17P GAIN WILD-TYPE 87  2   7  14  1   3  10   5 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           4      17        9       14       18         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P GAIN MUTATED           0         3         1          0          3
  17P GAIN WILD-TYPE        10         5         8          6         15
                    vv
clus                 STAGE IIIC STAGE IV
  17P GAIN MUTATED            1        1
  17P GAIN WILD-TYPE         22        5
D28V8, multiclass

Clustering(29) Variable = 17q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    8  9
  17Q GAIN WILD-TYPE 36 41
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 77 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 41 
$`17Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A3CE TCGA-D3-A3MV TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IC 
       16.47        13.32         5.39        36.69         4.93         6.64 
TCGA-EE-A181 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
        1.12         4.27         5.13         1.08         9.47        12.03 
TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-FR-A3YN TCGA-GN-A268 TCGA-GN-A26D 
        8.94         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-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       45.70        24.00         9.30         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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       44.52        25.15        22.36        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B 
       14.83        11.57         6.31         1.35        12.20        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       27.12         8.12         8.84         9.99         6.48         2.43 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D 
        8.09        11.31        25.28        23.90         9.67         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-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
        6.58        72.16         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
        6.41         0.20         1.02         0.13        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       31.33        84.72        10.09        16.21        12.16 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1.08               0.13 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             36.69              98.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              6.64              12.20 
[1] "1.1 - 36.7 (6.6)"  "0.1 - 98.8 (12.2)"
        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-A2JF         TCGA-D3-A2JK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "17Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "17Q GAIN MUTATED" 
[1] "hr=" "1.9"
D29V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q GAIN MUTATED                    2             0
  17Q GAIN WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q GAIN MUTATED                                                                                          5
  17Q GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  17Q GAIN MUTATED                    15
  17Q GAIN WILD-TYPE                  97
D29V3, multiclass
                                                                                          clus
vv                                                                                         17Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         17Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      97
D29V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     11   11
  17Q GAIN WILD-TYPE   56   95
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               11                 56
  MALE                 11                 95
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q GAIN MUTATED    19   0   1   0   0
  17Q GAIN WILD-TYPE 131   2   1   2   2
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  3  0
  17Q GAIN WILD-TYPE 83  2   7  14  1   2  10   4 13  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        2         1
  17Q GAIN WILD-TYPE           4      17        9       13       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q GAIN MUTATED           1         4         1          0          4
  17Q GAIN WILD-TYPE         9         4         8          6         14
                    vv
clus                 STAGE IIIC STAGE IV
  17Q GAIN MUTATED            3        1
  17Q GAIN WILD-TYPE         20        5
D29V8, multiclass

Clustering(30) Variable = 18p gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  9
  18P GAIN WILD-TYPE 39 41
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                14                 80 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 41 
$`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-FS-A4F2 TCGA-GN-A267 
        1.12        38.63         1.08        12.03         3.22        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
       21.14        11.41        30.87         6.35        15.25        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-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       51.12        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       14.83        11.57         6.31         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41        27.12         9.47         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         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-A3I3 
       72.16         8.81        53.82        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        15.39 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.08               0.13 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             45.70              98.76 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.01              11.13 
[1] "1.1 - 45.7 (14.0)" "0.1 - 98.8 (11.1)"
        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-A2JF         TCGA-D3-A2JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED"   "18P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-GN-A26D 
  "18P GAIN MUTATED" 
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P GAIN MUTATED                    4             0
  18P GAIN WILD-TYPE                 21             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P GAIN MUTATED                                                                                          5
  18P GAIN WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  18P GAIN MUTATED                    13
  18P GAIN WILD-TYPE                  99
D30V3, multiclass
                                                                                          clus
vv                                                                                         18P GAIN MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    13
                                                                                          clus
vv                                                                                         18P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       21
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      99
D30V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11   11
  18P GAIN WILD-TYPE   56   95
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                 56
  MALE                 11                 95
                    vv
clus                  M0  M1 M1A M1B M1C
  18P GAIN MUTATED    20   0   1   0   0
  18P GAIN WILD-TYPE 130   2   1   2   2
D30V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P GAIN MUTATED   13  0   3   2  0   1   0   0  3  0
  18P GAIN WILD-TYPE 82  2   4  14  1   3  11   5 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             2       3        0        0        2         0
  18P GAIN WILD-TYPE           2      14       10       14       17         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P GAIN MUTATED           0         6         1          3          2
  18P GAIN WILD-TYPE        10         2         8          3         16
                    vv
clus                 STAGE IIIC STAGE IV
  18P GAIN MUTATED            3        0
  18P GAIN WILD-TYPE         20        6
D30V8, multiclass

Clustering(31) Variable = 18q gain mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    3  5
  18Q GAIN WILD-TYPE 41 45
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 86 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 45 
$`18Q GAIN MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EE-A29L TCGA-FS-A4F2 TCGA-GN-A267 
       32.55        45.70        39.19         1.08         3.22        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I2 TCGA-DA-A1I4 
       48.79        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         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-A3I3 
       72.16         8.81        53.82        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        15.35        24.85        31.33        84.72 
TCGA-GN-A266 TCGA-GN-A268 
       10.09        15.39 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1.08               0.13 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             45.70              98.76 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            15.455             11.230 
[1] "1.1 - 45.7 (15.5)" "0.1 - 98.8 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "18Q GAIN MUTATED" 
[1] "hr=" "1"  
D31V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q GAIN MUTATED                    3             0
  18Q GAIN WILD-TYPE                 22             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q GAIN MUTATED                                                                                          4
  18Q GAIN WILD-TYPE                                                                                       31
                    vv
clus                 REGIONAL LYMPH NODE
  18Q GAIN MUTATED                     5
  18Q GAIN WILD-TYPE                 107
D31V3, multiclass
                                                                                          clus
vv                                                                                         18Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                4
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         18Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 31
  REGIONAL LYMPH NODE                                                                                     107
D31V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    6
  18Q GAIN WILD-TYPE   61  100
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                 61
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q GAIN MUTATED    11   0   0   0   0
  18Q GAIN WILD-TYPE 139   2   2   2   2
D31V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q GAIN MUTATED    8  0   2   0  0   0   0   0  2  0
  18Q GAIN WILD-TYPE 87  2   5  16  1   4  11   5 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             2       1        0        0        0         0
  18Q GAIN WILD-TYPE           2      16       10       14       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q GAIN MUTATED           0         5         0          2          0
  18Q GAIN WILD-TYPE        10         3         9          4         18
                    vv
clus                 STAGE IIIC STAGE IV
  18Q GAIN MUTATED            2        0
  18Q GAIN WILD-TYPE         21        6
D31V8, multiclass

Clustering(32) Variable = 19p gain mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    1  2
  19P GAIN WILD-TYPE 43 48
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 91 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 48 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q 
       38.63         4.41        27.12         9.47        12.03         8.12 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
        5.95        72.16         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
        6.41         0.20         1.02         0.13        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 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.08               0.13 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             32.55              98.76 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              8.84              11.57 
[1] "1.1 - 32.5 (8.8)"  "0.1 - 98.8 (11.6)"
        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-A2JF         TCGA-D3-A2JK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29N 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29N 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29D         TCGA-EE-A29E         TCGA-EE-A29H 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29L         TCGA-EE-A29M         TCGA-EE-A29N 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"19P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D32V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P GAIN MUTATED                    4             0
  19P GAIN WILD-TYPE                 21             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P GAIN MUTATED                                                                                          0
  19P GAIN WILD-TYPE                                                                                       35
                    vv
clus                 REGIONAL LYMPH NODE
  19P GAIN MUTATED                     7
  19P GAIN WILD-TYPE                 105
D32V3, multiclass
                                                                                          clus
vv                                                                                         19P GAIN MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                0
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         19P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       21
  PRIMARY TUMOR                                                                                             1
  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      5    6
  19P GAIN WILD-TYPE   62  100
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                5                 62
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  19P GAIN MUTATED    10   0   0   0   0
  19P GAIN WILD-TYPE 140   2   2   2   2
D32V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P GAIN MUTATED    8  0   0   1  0   0   0   0  1  0
  19P GAIN WILD-TYPE 87  2   7  15  1   4  11   5 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             2       2        0        1        0         1
  19P GAIN WILD-TYPE           2      15       10       13       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P GAIN MUTATED           1         1         0          0          0
  19P GAIN WILD-TYPE         9         7         9          6         18
                    vv
clus                 STAGE IIIC STAGE IV
  19P GAIN MUTATED            2        0
  19P GAIN WILD-TYPE         21        6
D32V8, multiclass

Clustering(33) Variable = 19q gain mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    3  4
  19Q GAIN WILD-TYPE 41 46
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 87 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                 46 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        8.81         7.96        37.97        11.15        38.63         4.41 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V 
       27.12         9.47        12.03         8.12         9.99         2.43 
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-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 
       78.44         1.71         5.95        72.16         8.81        53.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
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 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.08               0.13 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             32.55              98.76 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              8.84              11.57 
[1] "1.1 - 32.5 (8.8)"  "0.1 - 98.8 (11.6)"
        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-A2JF         TCGA-D3-A2JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D33V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q GAIN MUTATED                    4             0
  19Q GAIN WILD-TYPE                 21             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q GAIN MUTATED                                                                                          2
  19Q GAIN WILD-TYPE                                                                                       33
                    vv
clus                 REGIONAL LYMPH NODE
  19Q GAIN MUTATED                     9
  19Q GAIN WILD-TYPE                 103
D33V3, multiclass
                                                                                          clus
vv                                                                                         19Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         19Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       21
  PRIMARY TUMOR                                                                                             1
  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      9    6
  19Q GAIN WILD-TYPE   58  100
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                9                 58
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q GAIN MUTATED    14   0   0   0   0
  19Q GAIN WILD-TYPE 136   2   2   2   2
D33V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q GAIN MUTATED    8  0   1   2  0   0   0   0  2  1
  19Q GAIN WILD-TYPE 87  2   6  14  1   4  11   5 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             2       1        0        1        0         1
  19Q GAIN WILD-TYPE           2      16       10       13       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q GAIN MUTATED           2         1         1          1          0
  19Q GAIN WILD-TYPE         8         7         8          5         18
                    vv
clus                 STAGE IIIC STAGE IV
  19Q GAIN MUTATED            3        0
  19Q GAIN WILD-TYPE         20        6
D33V8, multiclass

Clustering(34) Variable = 20p gain mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   11 15
  20P GAIN WILD-TYPE 33 35
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                26                 68 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                 35 
$`20P GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JF TCGA-D3-A3CE TCGA-D3-A3MV 
       16.47        32.55        22.55        30.87        13.32         5.39 
TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A20H 
       10.03        13.68        36.69        17.56        36.07         8.81 
TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J 
        7.96         8.84        25.28         9.67         8.94         4.18 
TCGA-ER-A19L TCGA-ER-A19M TCGA-FR-A3YN TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A264 
       12.99        28.64         5.95         3.22         0.20        31.33 
TCGA-GN-A26A TCGA-GN-A26D 
       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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
        9.99        44.52        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D 
        1.35        12.20         4.27         5.13        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
        8.12         9.99         6.48         2.43         8.09        11.31 
TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       23.90         3.52        11.11        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-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 
        1.02         0.13        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 
              0.20               0.13 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             36.69              98.76 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            13.155             11.230 
[1] "0.2 - 36.7 (13.2)" "0.1 - 98.8 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-GN-A26D 
  "20P GAIN MUTATED" 
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P GAIN MUTATED                   10             0
  20P GAIN WILD-TYPE                 15             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P GAIN MUTATED                                                                                         12
  20P GAIN WILD-TYPE                                                                                       23
                    vv
clus                 REGIONAL LYMPH NODE
  20P GAIN MUTATED                    31
  20P GAIN WILD-TYPE                  81
D34V3, multiclass
                                                                                          clus
vv                                                                                         20P GAIN MUTATED
  DISTANT METASTASIS                                                                                     10
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               12
  REGIONAL LYMPH NODE                                                                                    31
                                                                                          clus
vv                                                                                         20P GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       15
  PRIMARY TUMOR                                                                                             1
  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     19   34
  20P GAIN WILD-TYPE   48   72
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               19                 48
  MALE                 34                 72
                    vv
clus                  M0  M1 M1A M1B M1C
  20P GAIN MUTATED    46   2   1   0   0
  20P GAIN WILD-TYPE 104   0   1   2   2
D34V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P GAIN MUTATED   31  0   4   3  0   2   3   2  4  1
  20P GAIN WILD-TYPE 64  2   3  13  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             2       6        6        4        5         2
  20P GAIN WILD-TYPE           2      11        4       10       14         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P GAIN MUTATED           1         4         2          3          5
  20P GAIN WILD-TYPE         9         4         7          3         13
                    vv
clus                 STAGE IIIC STAGE IV
  20P GAIN MUTATED            7        2
  20P GAIN WILD-TYPE         16        4
D34V8, multiclass

Clustering(35) Variable = 20q gain mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   16 17
  20Q GAIN WILD-TYPE 28 33
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                33                 61 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                17                 33 
$`20Q GAIN MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JF TCGA-D3-A3CE TCGA-D3-A3MV 
       16.47        32.55        22.55        30.87        13.32         5.39 
TCGA-DA-A1HV TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A3F5 
       48.79        10.03        13.68        36.69         4.93        17.56 
TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29P 
       36.07         8.81         7.96        38.63         1.08        12.03 
TCGA-EE-A29R TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L 
        8.84        25.28         9.67         8.94         4.18        12.99 
TCGA-ER-A19M TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F2 TCGA-FW-A3I3 
       28.64         1.71         5.95        72.16         3.22         0.20 
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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       44.52        25.15        22.36         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
        4.27         5.13        37.97        11.15         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        9.47         8.12         9.99         6.48         2.43         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-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 
        6.58         8.81        53.82        10.78         6.41         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.13        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 
       15.39 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.20               0.13 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             72.16              98.76 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             12.99              11.15 
[1] "0.2 - 72.2 (13.0)" "0.1 - 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-A2JF         TCGA-D3-A2JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "20Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "20Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "20Q GAIN MUTATED" "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-A182         TCGA-EE-A183 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "20Q GAIN MUTATED" 
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20Q GAIN MUTATED                   12             0
  20Q GAIN WILD-TYPE                 13             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20Q GAIN MUTATED                                                                                         14
  20Q GAIN WILD-TYPE                                                                                       21
                    vv
clus                 REGIONAL LYMPH NODE
  20Q GAIN MUTATED                    39
  20Q GAIN WILD-TYPE                  73
D35V3, multiclass
                                                                                          clus
vv                                                                                         20Q GAIN MUTATED
  DISTANT METASTASIS                                                                                     12
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               14
  REGIONAL LYMPH NODE                                                                                    39
                                                                                          clus
vv                                                                                         20Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       13
  PRIMARY TUMOR                                                                                             1
  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     23   42
  20Q GAIN WILD-TYPE   44   64
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               23                 44
  MALE                 42                 64
                    vv
clus                 M0 M1 M1A M1B M1C
  20Q GAIN MUTATED   54  2   2   1   0
  20Q GAIN WILD-TYPE 96  0   0   1   2
D35V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20Q GAIN MUTATED   35  0   4   6  0   2   4   2  6  1
  20Q GAIN WILD-TYPE 60  2   3  10  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             2       6        6        4        7         2
  20Q GAIN WILD-TYPE           2      11        4       10       12         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20Q GAIN MUTATED           1         5         3          3          8
  20Q GAIN WILD-TYPE         9         3         6          3         10
                    vv
clus                 STAGE IIIC STAGE IV
  20Q GAIN MUTATED            8        3
  20Q GAIN WILD-TYPE         15        3
D35V8, multiclass

Clustering(36) Variable = 21q gain mutation analysis
D36V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    7  8
  21Q GAIN WILD-TYPE 37 42
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                15                 79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 8                 42 
$`21Q GAIN MUTATED`
TCGA-D3-A3MV TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A2A0 
        5.39         8.81         7.96         1.08         8.84        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN 
       25.28         9.67         3.52        12.99         1.71         5.95 
TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A26D 
        3.22         0.20        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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z1 
       15.25        45.70        13.32        24.00         9.30         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        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-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       27.12         9.47        12.03         8.12         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J 
        2.43         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-FW-A3TU TCGA-GN-A261 
       53.82        10.78         6.41         1.02         0.13        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 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.20               0.13 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             25.28              98.76 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              7.96              13.32 
[1] "0.2 - 25.3 (8.0)"  "0.1 - 98.8 (13.3)"
        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-A2JF         TCGA-D3-A2JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "21Q GAIN MUTATED"   "21Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED"   "21Q GAIN MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-GN-A26D 
  "21Q GAIN MUTATED" 
[1] "hr=" "2.5"
D36V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q GAIN MUTATED                    4             0
  21Q GAIN WILD-TYPE                 21             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q GAIN MUTATED                                                                                          6
  21Q GAIN WILD-TYPE                                                                                       29
                    vv
clus                 REGIONAL LYMPH NODE
  21Q GAIN MUTATED                    11
  21Q GAIN WILD-TYPE                 101
D36V3, multiclass
                                                                                          clus
vv                                                                                         21Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      4
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         21Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       21
  PRIMARY TUMOR                                                                                             1
  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     10   11
  21Q GAIN WILD-TYPE   57   95
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               10                 57
  MALE                 11                 95
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q GAIN MUTATED    17   1   1   0   0
  21Q GAIN WILD-TYPE 133   1   1   2   2
D36V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q GAIN MUTATED   15  0   1   1  0   2   0   0  1  0
  21Q GAIN WILD-TYPE 80  2   6  15  1   2  11   5 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       2        0        4        1         3
  21Q GAIN WILD-TYPE           4      15       10       10       18         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q GAIN MUTATED           0         3         0          2          1
  21Q GAIN WILD-TYPE        10         5         9          4         17
                    vv
clus                 STAGE IIIC STAGE IV
  21Q GAIN MUTATED            2        2
  21Q GAIN WILD-TYPE         21        4
D36V8, multiclass

Clustering(37) Variable = 22q gain mutation analysis
D37V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   14 14
  22Q GAIN WILD-TYPE 30 36
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                28                 66 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                14                 36 
$`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-A1IA TCGA-DA-A1IB TCGA-DA-A3F5 
       39.19        36.69        25.15         4.93        22.36        17.56 
TCGA-EE-A20H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-ER-A19M 
        8.81         1.08        27.12         9.47         8.84        28.64 
TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-GN-A264 
        6.58         5.95        72.16         3.22         0.20        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       21.14        11.41        30.87         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY 
       13.32        24.00         4.01         2.86        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       13.68         9.99        44.52         6.64        19.36         7.00 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        4.27        36.07         5.13         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29T 
       38.63         4.41        12.03         8.12         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         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-A3PL TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC 
       78.44         1.71         8.81        53.82        10.78         6.41 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
        1.02         0.13        15.35        24.85        10.09        15.39 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.20               0.13 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             84.72              98.76 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            15.455             11.230 
[1] "0.2 - 84.7 (15.5)" "0.1 - 98.8 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "22Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "22Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "22Q GAIN MUTATED" "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-A29M         TCGA-EE-A29N 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED"   "22Q GAIN MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "22Q GAIN MUTATED"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-GN-A26D 
  "22Q GAIN MUTATED" 
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q GAIN MUTATED                    8             1
  22Q GAIN WILD-TYPE                 17             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q GAIN MUTATED                                                                                         13
  22Q GAIN WILD-TYPE                                                                                       22
                    vv
clus                 REGIONAL LYMPH NODE
  22Q GAIN MUTATED                    24
  22Q GAIN WILD-TYPE                  88
D37V3, multiclass
                                                                                          clus
vv                                                                                         22Q GAIN MUTATED
  DISTANT METASTASIS                                                                                      8
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               13
  REGIONAL LYMPH NODE                                                                                    24
                                                                                          clus
vv                                                                                         22Q GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                       17
  PRIMARY TUMOR                                                                                             0
  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     21   25
  22Q GAIN WILD-TYPE   46   81
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               21                 46
  MALE                 25                 81
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q GAIN MUTATED    39   1   1   1   0
  22Q GAIN WILD-TYPE 111   1   1   1   2
D37V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q GAIN MUTATED   20  0   4   3  0   3   3   3  7  0
  22Q GAIN WILD-TYPE 75  2   3  13  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       3        1        3        4         3
  22Q GAIN WILD-TYPE           4      14        9       11       15         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q GAIN MUTATED           0         4         3          5          6
  22Q GAIN WILD-TYPE        10         4         6          1         12
                    vv
clus                 STAGE IIIC STAGE IV
  22Q GAIN MUTATED            8        1
  22Q GAIN WILD-TYPE         15        5
D37V8, multiclass

Clustering(38) Variable = Xq gain mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    0  1
  XQ GAIN WILD-TYPE 44 49
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                93 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                49 
$`XQ GAIN MUTATED`
TCGA-GN-A264 
       31.33 

$`XQ 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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
       15.25        45.70        13.32        24.00         9.30         5.39 
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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        4.27        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.13        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 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33              0.13 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33             98.76 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            31.33             11.41 
[1] "31.3 - 31.3 (31.3)" "0.1 - 98.8 (11.4)" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                93 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A265 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" 
D38V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ GAIN MUTATED                    1             0
  XQ GAIN WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ GAIN MUTATED                                                                                          1
  XQ GAIN WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  XQ GAIN MUTATED                     1
  XQ GAIN WILD-TYPE                 111
D38V3, multiclass
                                                                                          clus
vv                                                                                         XQ GAIN MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         XQ GAIN WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    111
D38V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    3
  XQ GAIN WILD-TYPE   67  103
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               0                67
  MALE                 3               103
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ GAIN MUTATED     2   0   0   0   0
  XQ GAIN WILD-TYPE 148   2   2   2   2
D38V5, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               156 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A148        TCGA-D9-A149 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D9-A1JW        TCGA-D9-A1JX        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GD        TCGA-EE-A2GE        TCGA-EE-A2GH        TCGA-EE-A2GI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GJ        TCGA-EE-A2GK        TCGA-EE-A2GL        TCGA-EE-A2GM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GN        TCGA-EE-A2GO        TCGA-EE-A2GP        TCGA-EE-A2GR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2GU        TCGA-EE-A2M5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MD        TCGA-EE-A2ME        TCGA-EE-A2MG        TCGA-EE-A2MH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MK        TCGA-EE-A2ML 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A2MP        TCGA-EE-A2MQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-EE-A2MS        TCGA-EE-A2MT        TCGA-EE-A3AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19M        TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A3YO        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1YW        TCGA-FS-A1YX        TCGA-FS-A1YY        TCGA-FS-A1Z0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1Z7        TCGA-FS-A1ZA        TCGA-FS-A1ZB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZE        TCGA-FS-A1ZF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZG        TCGA-FS-A1ZH        TCGA-FS-A1ZJ        TCGA-FS-A1ZM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZP        TCGA-FS-A1ZQ        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZT        TCGA-FS-A1ZU        TCGA-FS-A1ZW        TCGA-FS-A1ZY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZZ        TCGA-FS-A4F0        TCGA-FS-A4F2        TCGA-FS-A4F9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  XQ GAIN MUTATED    2  0   0   0  0   0   0   0  0  0
  XQ GAIN WILD-TYPE 93  2   7  16  1   4  11   5 16  2
D38V6, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               157 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A148        TCGA-D9-A149 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D9-A1JW        TCGA-D9-A1JX        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-EE-A2GB        TCGA-EE-A2GC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GD        TCGA-EE-A2GE        TCGA-EE-A2GH        TCGA-EE-A2GI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GJ        TCGA-EE-A2GK        TCGA-EE-A2GL        TCGA-EE-A2GM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GN        TCGA-EE-A2GO        TCGA-EE-A2GP        TCGA-EE-A2GR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GS        TCGA-EE-A2GT        TCGA-EE-A2GU        TCGA-EE-A2M5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2M6        TCGA-EE-A2M7        TCGA-EE-A2M8        TCGA-EE-A2MC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MD        TCGA-EE-A2ME        TCGA-EE-A2MG        TCGA-EE-A2MH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MI        TCGA-EE-A2MJ        TCGA-EE-A2MK        TCGA-EE-A2ML 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MM        TCGA-EE-A2MN        TCGA-EE-A2MP        TCGA-EE-A2MQ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MR        TCGA-EE-A2MS        TCGA-EE-A2MT        TCGA-EE-A3AE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A3AH        TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19M        TCGA-ER-A19O        TCGA-ER-A1A1        TCGA-ER-A3ET 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A3YO        TCGA-FR-A44A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1YW        TCGA-FS-A1YX        TCGA-FS-A1YY        TCGA-FS-A1Z0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1Z4        TCGA-FS-A1Z7        TCGA-FS-A1ZA        TCGA-FS-A1ZB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZE        TCGA-FS-A1ZF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZG        TCGA-FS-A1ZH        TCGA-FS-A1ZJ        TCGA-FS-A1ZM 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZP        TCGA-FS-A1ZQ        TCGA-FS-A1ZR        TCGA-FS-A1ZS 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZT        TCGA-FS-A1ZU        TCGA-FS-A1ZW        TCGA-FS-A1ZY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZZ        TCGA-FS-A4F0        TCGA-FS-A4F2        TCGA-FS-A4F9 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TV 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A261        TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" 
D38V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ GAIN MUTATED             0       0        1        0        1         0
  XQ GAIN WILD-TYPE           4      17        9       14       18         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XQ GAIN MUTATED           0         0         0          0          0
  XQ GAIN WILD-TYPE        10         8         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  XQ GAIN MUTATED            0        0
  XQ GAIN WILD-TYPE         23        6
D38V8, multiclass
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2               150 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29V        TCGA-EE-A29X        TCGA-EE-A2A0 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A5        TCGA-EE-A2A6 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GB        TCGA-EE-A2GC        TCGA-EE-A2GD        TCGA-EE-A2GE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GH        TCGA-EE-A2GI        TCGA-EE-A2GJ        TCGA-EE-A2GK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GL        TCGA-EE-A2GM        TCGA-EE-A2GN        TCGA-EE-A2GO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GP        TCGA-EE-A2GR        TCGA-EE-A2GS        TCGA-EE-A2GT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2GU        TCGA-EE-A2M5        TCGA-EE-A2M6        TCGA-EE-A2M7 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2M8        TCGA-EE-A2MC        TCGA-EE-A2MD        TCGA-EE-A2ME 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MG        TCGA-EE-A2MH        TCGA-EE-A2MI        TCGA-EE-A2MJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MK        TCGA-EE-A2ML        TCGA-EE-A2MM        TCGA-EE-A2MN 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MP        TCGA-EE-A2MQ        TCGA-EE-A2MR        TCGA-EE-A2MS 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EE-A2MT        TCGA-EE-A3AE        TCGA-EE-A3AH        TCGA-ER-A19D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19M        TCGA-ER-A19O        TCGA-ER-A1A1 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A3YO 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1YW        TCGA-FS-A1YX        TCGA-FS-A1YY 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1Z0        TCGA-FS-A1Z4        TCGA-FS-A1Z7        TCGA-FS-A1ZA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZB        TCGA-FS-A1ZC        TCGA-FS-A1ZD        TCGA-FS-A1ZE 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZF        TCGA-FS-A1ZG        TCGA-FS-A1ZH        TCGA-FS-A1ZJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZM        TCGA-FS-A1ZP        TCGA-FS-A1ZQ        TCGA-FS-A1ZR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZS        TCGA-FS-A1ZT        TCGA-FS-A1ZU        TCGA-FS-A1ZW 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A1ZY        TCGA-FS-A1ZZ        TCGA-FS-A4F0        TCGA-FS-A4F2 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FW-A3TV        TCGA-GN-A261        TCGA-GN-A267        TCGA-GN-A268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 

Clustering(39) Variable = 1p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    3  4
  1P LOSS WILD-TYPE 41 46
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                87 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                46 
$`1P LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D3-A3CC TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A20H TCGA-ER-A19L 
       22.55        45.70        13.68        36.69         8.81        12.99 
TCGA-GN-A26D 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I4 
       48.79        35.80        51.12        10.03        39.19         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
        1.35        12.20         4.27        36.07         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        38.63         4.41         1.08        27.12 
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-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         8.09        11.31        25.28        23.90         9.67 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
        8.94         3.52        11.11         4.18        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       16.21        15.39        12.16 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             8.81              0.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            45.70             98.76 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            14.70             11.15 
[1] "8.8 - 45.7 (14.7)" "0.1 - 98.8 (11.2)"
       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-A2JF        TCGA-D3-A2JK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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-A4F2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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-A4F2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-D3-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-A2JF        TCGA-D3-A2JK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "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-A4F2 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
[1] "hr=" "1.3"
D39V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1P LOSS MUTATED                    1             0
  1P LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1P LOSS MUTATED                                                                                          4
  1P LOSS WILD-TYPE                                                                                       31
                   vv
clus                REGIONAL LYMPH NODE
  1P LOSS MUTATED                     8
  1P LOSS WILD-TYPE                 104
D39V3, multiclass
                                                                                          clus
vv                                                                                         1P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         1P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    104
D39V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    8
  1P LOSS WILD-TYPE   62   98
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                62
  MALE                 8                98
                   vv
clus                 M0  M1 M1A M1B M1C
  1P LOSS MUTATED    10   0   0   0   0
  1P LOSS WILD-TYPE 140   2   2   2   2
D39V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1P LOSS MUTATED    7  0   0   0  0   1   3   0  0  0
  1P LOSS WILD-TYPE 88  2   7  16  1   3   8   5 16  2
D39V6, multiclass
D39V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1P LOSS MUTATED             0       1        0        0        4         0
  1P LOSS WILD-TYPE           4      16       10       14       15         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1P LOSS MUTATED           0         2         1          0          2
  1P LOSS WILD-TYPE        10         6         8          6         16
                   vv
clus                STAGE IIIC STAGE IV
  1P LOSS MUTATED            1        0
  1P LOSS WILD-TYPE         22        6
D39V8, multiclass

Clustering(40) Variable = 1q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  4
  1Q LOSS WILD-TYPE 42 46
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                88 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                46 
$`1Q LOSS MUTATED`
TCGA-D3-A3CC TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EE-A20H TCGA-EE-A29X 
       45.70        13.68        36.69        25.15         8.81         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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        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-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
        9.99        44.52         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A 
        1.35        12.20         4.27        36.07         5.13         7.96 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
       37.97        11.15        38.63         4.41         1.08        27.12 
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-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
        2.43        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             8.09              0.13 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            45.70             98.76 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           19.415            11.360 
[1] "8.1 - 45.7 (19.4)" "0.1 - 98.8 (11.4)"
       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-A2JF        TCGA-D3-A2JK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "1Q LOSS MUTATED"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  1Q LOSS MUTATED                    1             0
  1Q LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  1Q LOSS MUTATED                                                                                          3
  1Q LOSS WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  1Q LOSS MUTATED                     2
  1Q LOSS WILD-TYPE                 110
D40V3, multiclass
                                                                                          clus
vv                                                                                         1Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         1Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    110
D40V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3    3
  1Q LOSS WILD-TYPE   64  103
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               3                64
  MALE                 3               103
                   vv
clus                 M0  M1 M1A M1B M1C
  1Q LOSS MUTATED     6   0   0   0   0
  1Q LOSS WILD-TYPE 144   2   2   2   2
D40V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  1Q LOSS MUTATED    3  0   0   0  0   0   2   0  1  0
  1Q LOSS WILD-TYPE 92  2   7  16  1   4   9   5 15  2
D40V6, multiclass
D40V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  1Q LOSS MUTATED             0       1        0        1        0         0
  1Q LOSS WILD-TYPE           4      16       10       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  1Q LOSS MUTATED           0         1         0          0          1
  1Q LOSS WILD-TYPE        10         7         9          6         17
                   vv
clus                STAGE IIIC STAGE IV
  1Q LOSS MUTATED            2        0
  1Q LOSS WILD-TYPE         21        6
D40V8, multiclass

Clustering(41) Variable = 2p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    4  4
  2P LOSS WILD-TYPE 40 46
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                8                86 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                46 
$`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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV 
       45.70        13.32         9.30         5.39         4.01        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        1.35        12.20         4.27         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.13        15.35        24.85        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A 
       15.39        12.16 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.86              0.13 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            36.07             98.76 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           14.975            11.230 
[1] "2.9 - 36.1 (15.0)" "0.1 - 98.8 (11.2)"
       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-A2JF        TCGA-D3-A2JK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2P LOSS MUTATED" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2P LOSS MUTATED                    1             0
  2P LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2P LOSS MUTATED                                                                                          2
  2P LOSS WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  2P LOSS MUTATED                    12
  2P LOSS WILD-TYPE                 100
D41V3, multiclass
                                                                                          clus
vv                                                                                         2P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   12
                                                                                          clus
vv                                                                                         2P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    100
D41V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    9
  2P LOSS WILD-TYPE   61   97
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               6                61
  MALE                 9                97
                   vv
clus                 M0  M1 M1A M1B M1C
  2P LOSS MUTATED    12   0   0   0   0
  2P LOSS WILD-TYPE 138   2   2   2   2
D41V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2P LOSS MUTATED   10  0   0   1  0   0   1   0  1  0
  2P LOSS WILD-TYPE 85  2   7  15  1   4  10   5 15  2
D41V6, multiclass
D41V7, 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         1
  2P LOSS WILD-TYPE           4      17       10       12       14         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         9         7         9          6         17
                   vv
clus                STAGE IIIC STAGE IV
  2P LOSS MUTATED            2        0
  2P LOSS WILD-TYPE         21        6
D41V8, multiclass

Clustering(42) Variable = 2q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    3  3
  2Q LOSS WILD-TYPE 41 47
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6                88 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                47 
$`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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
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-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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20H 
        6.31         1.12         1.35        12.20         4.27         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.96        37.97        38.63         4.41         1.08        27.12 
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-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        2.43         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        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 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5.13              0.13 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            36.07             98.76 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           14.975            11.360 
[1] "5.1 - 36.1 (15.0)" "0.1 - 98.8 (11.4)"
       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-A2JF        TCGA-D3-A2JK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "2Q LOSS MUTATED" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
[1] "hr=" "1.2"
D42V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  2Q LOSS MUTATED                    1             0
  2Q LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  2Q LOSS MUTATED                                                                                          2
  2Q LOSS WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  2Q LOSS MUTATED                    11
  2Q LOSS WILD-TYPE                 101
D42V3, multiclass
                                                                                          clus
vv                                                                                         2Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   11
                                                                                          clus
vv                                                                                         2Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    101
D42V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    7
  2Q LOSS WILD-TYPE   60   99
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               7                60
  MALE                 7                99
                   vv
clus                 M0  M1 M1A M1B M1C
  2Q LOSS MUTATED    11   0   0   1   0
  2Q LOSS WILD-TYPE 139   2   2   1   2
D42V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  2Q LOSS MUTATED   10  0   0   1  0   0   0   0  2  0
  2Q LOSS WILD-TYPE 85  2   7  15  1   4  11   5 14  2
D42V6, multiclass
D42V7, 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         1
  2Q LOSS WILD-TYPE           4      17       10       12       14         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         9         7         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  2Q LOSS MUTATED            2        0
  2Q LOSS WILD-TYPE         21        6
D42V8, multiclass

Clustering(43) Variable = 3p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    3  4
  3P LOSS WILD-TYPE 41 46
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                7                87 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                4                46 
$`3P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A3C6 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 
       32.55        15.25        48.79        35.80        13.68        36.69 
TCGA-GN-A262 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3CC 
        8.38        21.14        11.41        30.87         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-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       51.12        10.03        39.19         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        4.27        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.13        15.35        31.33        84.72        10.09        16.21 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       15.39        12.16        14.70 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            13.68              0.13 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            48.79             98.76 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            32.55             11.11 
[1] "13.7 - 48.8 (32.5)" "0.1 - 98.8 (11.1)" 
       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-A2JF        TCGA-D3-A2JK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3P LOSS MUTATED"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3P LOSS MUTATED                    1             0
  3P LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3P LOSS MUTATED                                                                                          5
  3P LOSS WILD-TYPE                                                                                       30
                   vv
clus                REGIONAL LYMPH NODE
  3P LOSS MUTATED                     6
  3P LOSS WILD-TYPE                 106
D43V3, multiclass
                                                                                          clus
vv                                                                                         3P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                    6
                                                                                          clus
vv                                                                                         3P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                30
  REGIONAL LYMPH NODE                                                                                    106
D43V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      5    7
  3P LOSS WILD-TYPE   62   99
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               5                62
  MALE                 7                99
                   vv
clus                 M0  M1 M1A M1B M1C
  3P LOSS MUTATED    10   0   0   0   0
  3P LOSS WILD-TYPE 140   2   2   2   2
D43V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3P LOSS MUTATED    5  0   0   1  0   0   3   1  0  0
  3P LOSS WILD-TYPE 90  2   7  15  1   4   8   4 16  2
D43V6, multiclass
D43V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3P LOSS MUTATED             2       2        0        1        0         0
  3P LOSS WILD-TYPE           2      15       10       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3P LOSS MUTATED           0         0         1          0          3
  3P LOSS WILD-TYPE        10         8         8          6         15
                   vv
clus                STAGE IIIC STAGE IV
  3P LOSS MUTATED            1        0
  3P LOSS WILD-TYPE         22        6
D43V8, multiclass

Clustering(44) Variable = 3q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    4  5
  3Q LOSS WILD-TYPE 40 45
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                85 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                45 
$`3Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-EE-A29H 
       32.55        48.79        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
        2.86        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       12.20         4.27        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        11.15        38.63         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        0.13        15.35        84.72        10.09        16.21        12.16 
TCGA-GN-A26D 
       14.70 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.41              0.13 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            48.79             98.76 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            31.33             11.11 
[1] "4.4 - 48.8 (31.3)" "0.1 - 98.8 (11.1)"
       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-A2JF        TCGA-D3-A2JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "3Q LOSS MUTATED"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED"   "3Q LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D44V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  3Q LOSS MUTATED                    0             0
  3Q LOSS WILD-TYPE                 25             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  3Q LOSS MUTATED                                                                                          4
  3Q LOSS WILD-TYPE                                                                                       31
                   vv
clus                REGIONAL LYMPH NODE
  3Q LOSS MUTATED                     8
  3Q LOSS WILD-TYPE                 104
D44V3, multiclass
                                                                                          clus
vv                                                                                         3Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                    8
                                                                                          clus
vv                                                                                         3Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      25
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                    104
D44V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6    6
  3Q LOSS WILD-TYPE   61  100
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               6                61
  MALE                 6               100
                   vv
clus                 M0  M1 M1A M1B M1C
  3Q LOSS MUTATED    10   0   0   0   0
  3Q LOSS WILD-TYPE 140   2   2   2   2
D44V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  3Q LOSS MUTATED    5  0   0   1  0   0   3   1  0  0
  3Q LOSS WILD-TYPE 90  2   7  15  1   4   8   4 16  2
D44V6, multiclass
D44V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  3Q LOSS MUTATED             1       1        2        0        0         0
  3Q LOSS WILD-TYPE           3      16        8       14       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  3Q LOSS MUTATED           1         0         1          0          3
  3Q LOSS WILD-TYPE         9         8         8          6         15
                   vv
clus                STAGE IIIC STAGE IV
  3Q LOSS MUTATED            1        0
  3Q LOSS WILD-TYPE         22        6
D44V8, multiclass

Clustering(45) Variable = 4p loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    4  5
  4P LOSS WILD-TYPE 40 45
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                85 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                45 
$`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-FW-A3TU TCGA-GN-A266 
        3.52         0.13        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       21.14        11.41        30.87         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
       24.00         9.30         5.39         4.01        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       12.20         4.27        36.07         5.13         8.81         7.96 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 
        3.22        10.78         6.41         0.20         1.02        15.35 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        31.33        84.72        16.21        15.39        12.16 
TCGA-GN-A26D 
       14.70 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.20 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            45.70             98.76 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            10.26             11.57 
[1] "0.1 - 45.7 (10.3)" "0.2 - 98.8 (11.6)"
       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-A2JF        TCGA-D3-A2JK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4P LOSS MUTATED                    4             0
  4P LOSS WILD-TYPE                 21             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4P LOSS MUTATED                                                                                          6
  4P LOSS WILD-TYPE                                                                                       29
                   vv
clus                REGIONAL LYMPH NODE
  4P LOSS MUTATED                     9
  4P LOSS WILD-TYPE                 103
D45V3, multiclass
                                                                                          clus
vv                                                                                         4P LOSS MUTATED
  DISTANT METASTASIS                                                                                     4
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                    9
                                                                                          clus
vv                                                                                         4P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      21
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                    103
D45V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     12    7
  4P LOSS WILD-TYPE   55   99
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              12                55
  MALE                 7                99
                   vv
clus                 M0  M1 M1A M1B M1C
  4P LOSS MUTATED    15   0   0   1   0
  4P LOSS WILD-TYPE 135   2   2   1   2
D45V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4P LOSS MUTATED   10  0   0   2  0   1   0   1  2  0
  4P LOSS WILD-TYPE 85  2   7  14  1   3  11   4 14  2
D45V6, multiclass
D45V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4P LOSS MUTATED             1       1        1        2        2         0
  4P LOSS WILD-TYPE           3      16        9       12       17         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4P LOSS MUTATED           1         2         0          1          3
  4P LOSS WILD-TYPE         9         6         9          5         15
                   vv
clus                STAGE IIIC STAGE IV
  4P LOSS MUTATED            1        0
  4P LOSS WILD-TYPE         22        6
D45V8, multiclass

Clustering(46) Variable = 4q loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    4  6
  4Q LOSS WILD-TYPE 40 44
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                84 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                44 
$`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-FW-A3TU TCGA-GN-A266 
       37.97         3.52         0.13        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       21.14        11.41        30.87         6.35        15.25        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
       24.00         9.30         5.39         4.01        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       25.15         4.93        22.36         6.64        19.36         7.00 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 
       17.56        14.83        11.57         6.31         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D 
        4.27        36.07         5.13         8.81         7.96        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19F 
       11.31        25.28        23.90         9.67         8.94        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-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 
       10.78         6.41         0.20         1.02        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       31.33        84.72        16.21        15.39        12.16        14.70 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.20 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            45.70             98.76 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.28             11.49 
[1] "0.1 - 45.7 (13.3)" "0.2 - 98.8 (11.5)"
       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-A2JF        TCGA-D3-A2JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  4Q LOSS MUTATED                    2             0
  4Q LOSS WILD-TYPE                 23             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  4Q LOSS MUTATED                                                                                          6
  4Q LOSS WILD-TYPE                                                                                       29
                   vv
clus                REGIONAL LYMPH NODE
  4Q LOSS MUTATED                    10
  4Q LOSS WILD-TYPE                 102
D46V3, multiclass
                                                                                          clus
vv                                                                                         4Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         4Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      23
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                    102
D46V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11    7
  4Q LOSS WILD-TYPE   56   99
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              11                56
  MALE                 7                99
                   vv
clus                 M0  M1 M1A M1B M1C
  4Q LOSS MUTATED    13   0   0   2   0
  4Q LOSS WILD-TYPE 137   2   2   0   2
D46V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  4Q LOSS MUTATED    9  0   0   2  0   1   0   0  3  0
  4Q LOSS WILD-TYPE 86  2   7  14  1   3  11   5 13  2
D46V6, multiclass
D46V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  4Q LOSS MUTATED             0       1        1        2        3         0
  4Q LOSS WILD-TYPE           4      16        9       12       16         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  4Q LOSS MUTATED           0         2         0          1          2
  4Q LOSS WILD-TYPE        10         6         9          5         16
                   vv
clus                STAGE IIIC STAGE IV
  4Q LOSS MUTATED            1        1
  4Q LOSS WILD-TYPE         22        5
D46V8, multiclass

Clustering(47) Variable = 5p loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    5  6
  5P LOSS WILD-TYPE 39 44
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11                83 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6                44 
$`5P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M 
       16.47        11.57         4.27        37.97        38.63        27.12 
TCGA-EE-A2A2 TCGA-FS-A4F2 TCGA-GN-A262 TCGA-GN-A266 TCGA-GN-A268 
       23.90         3.22        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F 
        6.31         1.12         1.35        12.20        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N 
        8.81         7.96        11.15         4.41         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        15.35 
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 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3.22              0.13 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            38.63             98.76 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            16.47             11.15 
[1] "3.2 - 38.6 (16.5)" "0.1 - 98.8 (11.2)"
       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-A2JF        TCGA-D3-A2JK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5P LOSS MUTATED                    3             1
  5P LOSS WILD-TYPE                 22             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5P LOSS MUTATED                                                                                          4
  5P LOSS WILD-TYPE                                                                                       31
                   vv
clus                REGIONAL LYMPH NODE
  5P LOSS MUTATED                    15
  5P LOSS WILD-TYPE                  97
D47V3, multiclass
                                                                                          clus
vv                                                                                         5P LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               4
  REGIONAL LYMPH NODE                                                                                   15
                                                                                          clus
vv                                                                                         5P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                31
  REGIONAL LYMPH NODE                                                                                     97
D47V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9   14
  5P LOSS WILD-TYPE   58   92
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               9                58
  MALE                14                92
                   vv
clus                 M0  M1 M1A M1B M1C
  5P LOSS MUTATED    19   0   0   0   0
  5P LOSS WILD-TYPE 131   2   2   2   2
D47V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5P LOSS MUTATED   11  0   0   3  0   1   1   1  2  0
  5P LOSS WILD-TYPE 84  2   7  13  1   3  10   4 14  2
D47V6, multiclass
D47V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5P LOSS MUTATED             0       2        2        2        1         1
  5P LOSS WILD-TYPE           4      15        8       12       18         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5P LOSS MUTATED           2         1         2          1          2
  5P LOSS WILD-TYPE         8         7         7          5         16
                   vv
clus                STAGE IIIC STAGE IV
  5P LOSS MUTATED            3        0
  5P LOSS WILD-TYPE         20        6
D47V8, multiclass

Clustering(48) Variable = 5q loss mutation analysis
D48V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    8 12
  5Q LOSS WILD-TYPE 36 38
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               20                74 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12                38 
$`5Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D9-A3Z1 TCGA-DA-A1HW 
       28.08         6.35        15.25        24.00         4.01        35.80 
TCGA-DA-A1I0 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-EE-A17X TCGA-EE-A185 TCGA-EE-A20H 
       10.03        44.52        36.69        11.57         4.27         8.81 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A2A2 TCGA-GN-A262 
       37.97        38.63        27.12         2.43        23.90        24.85 
TCGA-GN-A266 TCGA-GN-A268 
       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-A2JF TCGA-D3-A3CC TCGA-D3-A3CE 
        8.38        21.14        11.41        30.87        45.70        13.32 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 
        9.30         5.39         2.86        48.79        51.12        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       13.68         9.99        25.15         4.93        22.36         6.64 
TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A181 
       19.36         7.00        17.56        14.83         6.31         1.12 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A29A TCGA-EE-A29D 
        1.35        12.20        36.07         5.13         7.96        11.15 
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-A2A5 
        9.99         6.48         8.09        11.31        25.28         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        1.02         0.13        15.35        31.33        84.72        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.43              0.13 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            44.52             98.76 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           19.645            11.130 
[1] "2.4 - 44.5 (19.6)" "0.1 - 98.8 (11.1)"
       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-A2JF        TCGA-D3-A2JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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-A4F2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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-A4F2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       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-A4F2 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  5Q LOSS MUTATED                    7             1
  5Q LOSS WILD-TYPE                 18             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  5Q LOSS MUTATED                                                                                          6
  5Q LOSS WILD-TYPE                                                                                       29
                   vv
clus                REGIONAL LYMPH NODE
  5Q LOSS MUTATED                    23
  5Q LOSS WILD-TYPE                  89
D48V3, multiclass
                                                                                          clus
vv                                                                                         5Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     7
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   23
                                                                                          clus
vv                                                                                         5Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      18
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                29
  REGIONAL LYMPH NODE                                                                                     89
D48V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13   24
  5Q LOSS WILD-TYPE   54   82
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13                54
  MALE                24                82
                   vv
clus                 M0  M1 M1A M1B M1C
  5Q LOSS MUTATED    30   0   1   1   1
  5Q LOSS WILD-TYPE 120   2   1   1   1
D48V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  5Q LOSS MUTATED   17  0   0   5  0   1   3   1  5  1
  5Q LOSS WILD-TYPE 78  2   7  11  1   3   8   4 11  1
D48V6, multiclass
D48V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  5Q LOSS MUTATED             2       4        2        3        3         1
  5Q LOSS WILD-TYPE           2      13        8       11       16         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  5Q LOSS MUTATED           1         0         2          1          4
  5Q LOSS WILD-TYPE         9         8         7          5         14
                   vv
clus                STAGE IIIC STAGE IV
  5Q LOSS MUTATED            7        2
  5Q LOSS WILD-TYPE         16        4
D48V8, multiclass

Clustering(49) Variable = 6p loss mutation analysis
D49V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    4  7
  6P LOSS WILD-TYPE 40 43
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11                83 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                43 
$`6P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29D 
       32.55        22.55        10.26        51.12        25.15        11.15 
TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
       27.12         8.12         8.09        11.31        25.28 

$`6P LOSS WILD-TYPE`
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 
       16.47        70.16        98.76        28.08         8.38        21.14 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE 
       11.41        30.87         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-A1I5 
       35.80        10.03        39.19        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69         4.93        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-A182 
       17.56        14.83        11.57         6.31         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       12.20         4.27        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P 
       37.97        38.63         4.41         1.08         9.47        12.03 
TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99         6.48         2.43        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        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 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             8.09              0.13 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            51.12             98.76 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            22.55             11.41 
[1] "8.1 - 51.1 (22.6)" "0.1 - 98.8 (11.4)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "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-A2JF        TCGA-D3-A2JK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6P LOSS WILD-TYPE" "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 MUTATED" "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-A4F2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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 MUTATED" "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-A2JF        TCGA-D3-A2JK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6P LOSS WILD-TYPE" "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 MUTATED" "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-A4F2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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 MUTATED" "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-A2JF        TCGA-D3-A2JK 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6P LOSS WILD-TYPE" "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 MUTATED" "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-A4F2 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6P LOSS MUTATED                    3             1
  6P LOSS WILD-TYPE                 22             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6P LOSS MUTATED                                                                                          3
  6P LOSS WILD-TYPE                                                                                       32
                   vv
clus                REGIONAL LYMPH NODE
  6P LOSS MUTATED                    10
  6P LOSS WILD-TYPE                 102
D49V3, multiclass
                                                                                          clus
vv                                                                                         6P LOSS MUTATED
  DISTANT METASTASIS                                                                                     3
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               3
  REGIONAL LYMPH NODE                                                                                   10
                                                                                          clus
vv                                                                                         6P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      22
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                32
  REGIONAL LYMPH NODE                                                                                    102
D49V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6   11
  6P LOSS WILD-TYPE   61   95
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               6                61
  MALE                11                95
                   vv
clus                 M0  M1 M1A M1B M1C
  6P LOSS MUTATED    17   0   0   0   0
  6P LOSS WILD-TYPE 133   2   2   2   2
D49V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6P LOSS MUTATED   12  0   0   2  0   1   0   0  2  0
  6P LOSS WILD-TYPE 83  2   7  14  1   3  11   5 14  2
D49V6, multiclass
D49V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6P LOSS MUTATED             2       1        0        4        2         1
  6P LOSS WILD-TYPE           2      16       10       10       17         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6P LOSS MUTATED           2         0         1          0          1
  6P LOSS WILD-TYPE         8         8         8          6         17
                   vv
clus                STAGE IIIC STAGE IV
  6P LOSS MUTATED            3        0
  6P LOSS WILD-TYPE         20        6
D49V8, multiclass

Clustering(50) Variable = 6q loss mutation analysis
D50V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   19 24
  6Q LOSS WILD-TYPE 25 26
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               43                51 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               24                26 
$`6Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A3C6 
       16.47        32.55        22.55        10.26        30.87        15.25 
TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I7 
        2.86        48.79        51.12        39.19         9.99        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A20B 
       25.15         6.64        17.56         1.35         4.27        36.07 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29M 
        8.81         7.96        37.97        11.15         4.41        27.12 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        8.12         9.99         2.43         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-A3I3 TCGA-FW-A3R5 TCGA-GN-A267 TCGA-GN-A268 
        1.71         8.81         0.20         1.02        16.21        15.39 
TCGA-GN-A26A 
       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-A1I5 TCGA-DA-A1IA 
        4.01        35.80        10.03        13.68        44.52         4.93 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
       22.36        19.36         7.00        14.83        11.57         6.31 
TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
        1.12        12.20         5.13        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
       12.03         8.84         6.48        12.99        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F2 
       78.44         6.58         5.95        72.16        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       10.78         6.41         0.13        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       84.72        10.09        14.70 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.20              0.13 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            51.12             98.76 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            11.11             12.20 
[1] "0.2 - 51.1 (11.1)" "0.1 - 98.8 (12.2)"
       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-A2JF        TCGA-D3-A2JK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       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-A4F2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       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-A4F2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
  "6Q LOSS MUTATED"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       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-A4F2 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED"   "6Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D50V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  6Q LOSS MUTATED                   13             1
  6Q LOSS WILD-TYPE                 12             0
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  6Q LOSS MUTATED                                                                                         17
  6Q LOSS WILD-TYPE                                                                                       18
                   vv
clus                REGIONAL LYMPH NODE
  6Q LOSS MUTATED                    38
  6Q LOSS WILD-TYPE                  74
D50V3, multiclass
                                                                                          clus
vv                                                                                         6Q LOSS MUTATED
  DISTANT METASTASIS                                                                                    13
  PRIMARY TUMOR                                                                                          1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              17
  REGIONAL LYMPH NODE                                                                                   38
                                                                                          clus
vv                                                                                         6Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      12
  PRIMARY TUMOR                                                                                            0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                18
  REGIONAL LYMPH NODE                                                                                     74
D50V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27   42
  6Q LOSS WILD-TYPE   40   64
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              27                40
  MALE                42                64
                   vv
clus                M0 M1 M1A M1B M1C
  6Q LOSS MUTATED   61  2   1   1   1
  6Q LOSS WILD-TYPE 89  0   1   1   1
D50V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  6Q LOSS MUTATED   37  0   4   7  1   1   4   3  8  1
  6Q LOSS WILD-TYPE 58  2   3   9  0   3   7   2  8  1
D50V6, multiclass
D50V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  6Q LOSS MUTATED             3       4        5        8        6         2
  6Q LOSS WILD-TYPE           1      13        5        6       13         6
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  6Q LOSS MUTATED           4         2         3          3          9
  6Q LOSS WILD-TYPE         6         6         6          3          9
                   vv
clus                STAGE IIIC STAGE IV
  6Q LOSS MUTATED           10        4
  6Q LOSS WILD-TYPE         13        2
D50V8, multiclass

Clustering(51) Variable = 7p loss mutation analysis
D51V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    0  2
  7P LOSS WILD-TYPE 44 48
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                92 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                48 
$`7P LOSS MUTATED`
TCGA-D3-A3CE TCGA-EE-A2A5 
       13.32         9.67 

$`7P 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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       11.31        25.28        23.90         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-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             9.67              0.13 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.32             98.76 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           11.495            11.490 
[1] "9.7 - 13.3 (11.5)" "0.1 - 98.8 (11.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "7P LOSS MUTATED"       
clus
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                92 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB        TCGA-DA-A1IC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A182 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B        TCGA-EE-A20F 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29M 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V        TCGA-EE-A29X 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FS-A4F0        TCGA-FS-A4F2        TCGA-FS-A4F9        TCGA-FS-A4FC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TU        TCGA-GN-A261 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
D51V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7P LOSS MUTATED                    1             0
  7P LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7P LOSS MUTATED                                                                                          1
  7P LOSS WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  7P LOSS MUTATED                     1
  7P LOSS WILD-TYPE                 111
D51V3, multiclass
                                                                                          clus
vv                                                                                         7P LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         7P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    111
D51V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE   65  105
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               2                65
  MALE                 1               105
                   vv
clus                 M0  M1 M1A M1B M1C
  7P LOSS MUTATED     3   0   0   0   0
  7P LOSS WILD-TYPE 147   2   2   2   2
D51V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7P LOSS MUTATED    2  0   0   1  0   0   0   0  0  0
  7P LOSS WILD-TYPE 93  2   7  15  1   4  11   5 16  2
D51V6, multiclass
D51V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7P LOSS MUTATED             0       0        0        1        0         0
  7P LOSS WILD-TYPE           4      17       10       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7P LOSS MUTATED           0         1         1          0          0
  7P LOSS WILD-TYPE        10         7         8          6         18
                   vv
clus                STAGE IIIC STAGE IV
  7P LOSS MUTATED            0        0
  7P LOSS WILD-TYPE         23        6
D51V8, multiclass

Clustering(52) Variable = 7q loss mutation analysis
D52V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    0  2
  7Q LOSS WILD-TYPE 44 48
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                92 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                48 
$`7Q LOSS MUTATED`
TCGA-D3-A3CE TCGA-EE-A2A5 
       13.32         9.67 

$`7Q 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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
       36.07         5.13         8.81         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       38.63         4.41         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X 
        8.12         8.84         9.99         6.48         2.43         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       11.31        25.28        23.90         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-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             9.67              0.13 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.32             98.76 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           11.495            11.490 
[1] "9.7 - 13.3 (11.5)" "0.1 - 98.8 (11.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                92 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-D3-A3MO 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3        TCGA-DA-A1HV 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0        TCGA-DA-A1I1 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5        TCGA-DA-A1I7 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB        TCGA-DA-A1IC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5        TCGA-DA-A3F8 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181        TCGA-EE-A182 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B        TCGA-EE-A20F 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C        TCGA-EE-A29D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L        TCGA-EE-A29M 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q        TCGA-EE-A29R 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V        TCGA-EE-A29X 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2        TCGA-EE-A2A6 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19D        TCGA-ER-A19F        TCGA-ER-A19J        TCGA-ER-A19L 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A19M        TCGA-ER-A19N        TCGA-ER-A1A1        TCGA-ER-A3ET 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-ER-A3PL        TCGA-FR-A3YN        TCGA-FR-A44A        TCGA-FS-A1ZR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FS-A4F0        TCGA-FS-A4F2        TCGA-FS-A4F9        TCGA-FS-A4FC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FW-A3I3        TCGA-FW-A3R5        TCGA-FW-A3TU        TCGA-GN-A261 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A262        TCGA-GN-A264        TCGA-GN-A265        TCGA-GN-A266 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-GN-A267        TCGA-GN-A268        TCGA-GN-A26A        TCGA-GN-A26D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
D52V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  7Q LOSS MUTATED                    1             0
  7Q LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  7Q LOSS MUTATED                                                                                          1
  7Q LOSS WILD-TYPE                                                                                       34
                   vv
clus                REGIONAL LYMPH NODE
  7Q LOSS MUTATED                     1
  7Q LOSS WILD-TYPE                 111
D52V3, multiclass
                                                                                          clus
vv                                                                                         7Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
  REGIONAL LYMPH NODE                                                                                    1
                                                                                          clus
vv                                                                                         7Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                34
  REGIONAL LYMPH NODE                                                                                    111
D52V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE   65  105
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                65
  MALE                 1               105
                   vv
clus                 M0  M1 M1A M1B M1C
  7Q LOSS MUTATED     3   0   0   0   0
  7Q LOSS WILD-TYPE 147   2   2   2   2
D52V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  7Q LOSS MUTATED    2  0   0   1  0   0   0   0  0  0
  7Q LOSS WILD-TYPE 93  2   7  15  1   4  11   5 16  2
D52V6, multiclass
D52V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  7Q LOSS MUTATED             0       0        0        1        0         0
  7Q LOSS WILD-TYPE           4      17       10       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  7Q LOSS MUTATED           0         1         1          0          0
  7Q LOSS WILD-TYPE        10         7         8          6         18
                   vv
clus                STAGE IIIC STAGE IV
  7Q LOSS MUTATED            0        0
  7Q LOSS WILD-TYPE         23        6
D52V8, multiclass

Clustering(53) Variable = 8p loss mutation analysis
D53V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    2  7
  8P LOSS WILD-TYPE 42 43
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                9                85 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                43 
$`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-A29V TCGA-EE-A2A5 TCGA-GN-A264 
        2.43         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-A2JF TCGA-D3-A2JK TCGA-D3-A3CC 
        8.38        21.14        11.41        30.87         6.35        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HV 
       13.32        24.00         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.12         1.35         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        7.96        11.15        38.63         1.08        27.12         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-A2A6 TCGA-ER-A19D TCGA-ER-A19F 
       11.31        25.28        23.90         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-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        15.35 
TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       24.85        84.72        10.09        16.21        15.39        12.16 
TCGA-GN-A26D 
       14.70 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             2.43              0.13 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            37.97             98.76 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            12.20             11.41 
[1] "2.4 - 38.0 (12.2)" "0.1 - 98.8 (11.4)"
       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-A2JF        TCGA-D3-A2JK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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-A4F2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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-A4F2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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-A4F2 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D53V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8P LOSS MUTATED                    6             0
  8P LOSS WILD-TYPE                 19             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8P LOSS MUTATED                                                                                          2
  8P LOSS WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  8P LOSS MUTATED                    14
  8P LOSS WILD-TYPE                  98
D53V3, multiclass
                                                                                          clus
vv                                                                                         8P LOSS MUTATED
  DISTANT METASTASIS                                                                                     6
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                   14
                                                                                          clus
vv                                                                                         8P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      19
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                     98
D53V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8   14
  8P LOSS WILD-TYPE   59   92
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               8                59
  MALE                14                92
                   vv
clus                 M0  M1 M1A M1B M1C
  8P LOSS MUTATED    18   0   0   1   0
  8P LOSS WILD-TYPE 132   2   2   1   2
D53V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8P LOSS MUTATED   12  0   0   2  0   1   0   2  2  0
  8P LOSS WILD-TYPE 83  2   7  14  1   3  11   3 14  2
D53V6, multiclass
D53V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8P LOSS MUTATED             1       4        2        3        1         1
  8P LOSS WILD-TYPE           3      13        8       11       18         7
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8P LOSS MUTATED           0         0         2          0          1
  8P LOSS WILD-TYPE        10         8         7          6         17
                   vv
clus                STAGE IIIC STAGE IV
  8P LOSS MUTATED            2        0
  8P LOSS WILD-TYPE         21        6
D53V8, multiclass

Clustering(54) Variable = 8q loss mutation analysis
D54V1, survival
                   sevent
clus2                0  1
  8Q LOSS WILD-TYPE 44 50
8Q LOSS WILD-TYPE 
               94 
[1] 50
$`8Q 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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV 
       15.25        45.70        13.32        24.00         9.30         5.39 
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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        4.27        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       11.15        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

8Q LOSS WILD-TYPE 
             0.13 
8Q LOSS WILD-TYPE 
            98.76 
8Q LOSS WILD-TYPE 
            11.49 
[1] "0.1 - 98.8 (11.5)"
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q1        TCGA-D3-A1Q5        TCGA-D3-A1Q6        TCGA-D3-A1Q7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A1Q8        TCGA-D3-A1Q9        TCGA-D3-A2J6        TCGA-D3-A2J8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A2J9        TCGA-D3-A2JD        TCGA-D3-A2JF        TCGA-D3-A2JK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A29X        TCGA-EE-A2A0        TCGA-EE-A2A1        TCGA-EE-A2A2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EE-A2A5        TCGA-EE-A2A6        TCGA-ER-A19D        TCGA-ER-A19F 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A19J        TCGA-ER-A19L        TCGA-ER-A19M        TCGA-ER-A19N 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-ER-A3PL        TCGA-FR-A3YN 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FR-A44A        TCGA-FS-A1ZR        TCGA-FS-A4F0        TCGA-FS-A4F2 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
D54V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  8Q LOSS MUTATED                    1             0
  8Q LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  8Q LOSS MUTATED                                                                                          0
  8Q LOSS WILD-TYPE                                                                                       35
                   vv
clus                REGIONAL LYMPH NODE
  8Q LOSS MUTATED                     2
  8Q LOSS WILD-TYPE                 110
D54V3, multiclass
                                                                                          clus
vv                                                                                         8Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    2
                                                                                          clus
vv                                                                                         8Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                35
  REGIONAL LYMPH NODE                                                                                    110
D54V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    0
  8Q LOSS WILD-TYPE   64  106
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                64
  MALE                 0               106
                   vv
clus                 M0  M1 M1A M1B M1C
  8Q LOSS MUTATED     3   0   0   0   0
  8Q LOSS WILD-TYPE 147   2   2   2   2
D54V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  8Q LOSS MUTATED    2  0   0   0  0   0   0   1  0  0
  8Q LOSS WILD-TYPE 93  2   7  16  1   4  11   4 16  2
D54V6, multiclass
D54V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  8Q LOSS MUTATED             0       2        0        0        0         0
  8Q LOSS WILD-TYPE           4      15       10       14       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  8Q LOSS MUTATED           0         0         0          0          1
  8Q LOSS WILD-TYPE        10         8         9          6         17
                   vv
clus                STAGE IIIC STAGE IV
  8Q LOSS MUTATED            0        0
  8Q LOSS WILD-TYPE         23        6
D54V8, multiclass

Clustering(55) Variable = 9p loss mutation analysis
D55V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   22 35
  9P LOSS WILD-TYPE 22 15
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               57                37 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               35                15 
$`9P LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J6 TCGA-D3-A2JF 
       16.47        32.55        70.16        28.08        10.26        30.87 
TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D9-A3Z3 TCGA-DA-A1HV 
        6.35        15.25        24.00         9.30         2.86        48.79 
TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 
       35.80        51.12        39.19        13.68         9.99        44.52 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       25.15         4.93         6.64        11.57         1.12         1.35 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29D 
        4.27        36.07         5.13         8.81        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S 
       38.63         1.08         9.47        12.03         8.12         9.99 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19F 
        2.43         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       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-A29A TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A2A1 
        7.96         4.41        27.12         8.84         6.48        25.28 
TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET 
       23.90         8.94         4.18        42.84        78.44         6.58 
TCGA-FR-A44A TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
       72.16        15.35        24.85        31.33        84.72        10.09 
TCGA-GN-A267 
       16.21 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              4.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            70.16             98.76 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.78             15.35 
[1] "0.1 - 70.2 (10.8)" "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-A2JF        TCGA-D3-A2JK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       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-A4F2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       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-A4F2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       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-A4F2 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
  "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9P LOSS MUTATED"   "9P LOSS MUTATED" 
[1] "hr=" "1.9"
D55V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9P LOSS MUTATED                   18             0
  9P LOSS WILD-TYPE                  7             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9P LOSS MUTATED                                                                                         25
  9P LOSS WILD-TYPE                                                                                       10
                   vv
clus                REGIONAL LYMPH NODE
  9P LOSS MUTATED                    57
  9P LOSS WILD-TYPE                  55
D55V3, multiclass
                                                                                          clus
vv                                                                                         9P LOSS MUTATED
  DISTANT METASTASIS                                                                                    18
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              25
  REGIONAL LYMPH NODE                                                                                   57
                                                                                          clus
vv                                                                                         9P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       7
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                10
  REGIONAL LYMPH NODE                                                                                     55
D55V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     40   60
  9P LOSS WILD-TYPE   27   46
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              40                27
  MALE                60                46
                   vv
clus                M0 M1 M1A M1B M1C
  9P LOSS MUTATED   86  1   1   2   2
  9P LOSS WILD-TYPE 64  1   1   0   0
D55V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9P LOSS MUTATED   58  0   4  11  1   0   4   5 10  0
  9P LOSS WILD-TYPE 37  2   3   5  0   4   7   0  6  2
D55V6, multiclass
D55V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9P LOSS MUTATED             4       4        4        9       14         6
  9P LOSS WILD-TYPE           0      13        6        5        5         2
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9P LOSS MUTATED           7         5         4          2         11
  9P LOSS WILD-TYPE         3         3         5          4          7
                   vv
clus                STAGE IIIC STAGE IV
  9P LOSS MUTATED           14        5
  9P LOSS WILD-TYPE          9        1
D55V8, multiclass

Clustering(56) Variable = 9q loss mutation analysis
D56V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   16 24
  9Q LOSS WILD-TYPE 28 26
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               40                54 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               24                26 
$`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-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IA 
       39.19        13.68         9.99        44.52        25.15         4.93 
TCGA-DA-A1IC TCGA-EE-A181 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29D 
        6.64         1.12        36.07         5.13         8.81        11.15 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
        1.08         9.47        12.03         8.12         9.99         8.09 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19M TCGA-ER-A3PL 
       11.31        23.90         3.52        11.11        28.64         1.71 
TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
        8.81        53.82         3.22         6.41         0.20         1.02 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       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-A2JF TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       11.41        30.87         6.35        45.70        13.32        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HY TCGA-DA-A1I0 
        9.30         5.39         4.01         2.86        51.12        10.03 
TCGA-DA-A1I7 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
       36.69        22.36        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A29A 
       11.57         6.31         1.35        12.20         4.27         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29R TCGA-EE-A29T 
       37.97        38.63         4.41        27.12         8.84         6.48 
TCGA-EE-A29V TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19J TCGA-ER-A19L 
        2.43        25.28         9.67         8.94         4.18        12.99 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FS-A4F9 
       42.84        78.44         6.58         5.95        72.16        10.78 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 
        0.13        15.35        31.33        84.72        10.09        16.21 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.20              0.13 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            53.82             98.76 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           11.230            11.885 
[1] "0.2 - 53.8 (11.2)" "0.1 - 98.8 (11.9)"
       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-A2JF        TCGA-D3-A2JK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "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-A4F2 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "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-A4F2 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "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-A2JF        TCGA-D3-A2JK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A182        TCGA-EE-A183        TCGA-EE-A185        TCGA-EE-A20B 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A20F        TCGA-EE-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "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-A4F2 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-GN-A26A        TCGA-GN-A26D 
  "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  9Q LOSS MUTATED                   14             0
  9Q LOSS WILD-TYPE                 11             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  9Q LOSS MUTATED                                                                                         19
  9Q LOSS WILD-TYPE                                                                                       16
                   vv
clus                REGIONAL LYMPH NODE
  9Q LOSS MUTATED                    42
  9Q LOSS WILD-TYPE                  70
D56V3, multiclass
                                                                                          clus
vv                                                                                         9Q LOSS MUTATED
  DISTANT METASTASIS                                                                                    14
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              19
  REGIONAL LYMPH NODE                                                                                   42
                                                                                          clus
vv                                                                                         9Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      11
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                16
  REGIONAL LYMPH NODE                                                                                     70
D56V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     36   39
  9Q LOSS WILD-TYPE   31   67
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              36                31
  MALE                39                67
                   vv
clus                M0 M1 M1A M1B M1C
  9Q LOSS MUTATED   62  1   1   2   2
  9Q LOSS WILD-TYPE 88  1   1   0   0
D56V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  9Q LOSS MUTATED   44  0   4   5  1   1   4   4  6  0
  9Q LOSS WILD-TYPE 51  2   3  11  0   3   7   1 10  2
D56V6, multiclass
D56V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  9Q LOSS MUTATED             3       2        2        6       10         4
  9Q LOSS WILD-TYPE           1      15        8        8        9         4
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  9Q LOSS MUTATED           7         5         3          3          9
  9Q LOSS WILD-TYPE         3         3         6          3          9
                   vv
clus                STAGE IIIC STAGE IV
  9Q LOSS MUTATED            6        5
  9Q LOSS WILD-TYPE         17        1
D56V8, multiclass

Clustering(57) Variable = 10p loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   13 27
  10P LOSS WILD-TYPE 31 23
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                 54 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                27                 23 
$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29H 
        6.31         4.27        36.07         5.13         8.81         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29X TCGA-EE-A2A5 TCGA-ER-A19D 
        1.08        27.12        12.03         8.09         9.67         3.52 
TCGA-ER-A19L TCGA-ER-A3ET TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A1ZR TCGA-GN-A264 
       12.99         6.58         1.71         5.95         8.81        31.33 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       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-A2JF 
       22.55        10.26         8.38        21.14        11.41        30.87 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY 
       15.25        45.70         5.39         4.01        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
       10.03        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29A 
       14.83        11.57         1.12         1.35        12.20         7.96 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R 
       37.97        11.15        38.63         9.47         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         2.43        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 
        8.94        11.11         4.18        28.64        42.84        78.44 
TCGA-FR-A44A TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       72.16        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D 
        1.02         0.13        15.35        24.85        84.72        14.70 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.08               0.13 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             98.76              84.72 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.095             11.360 
[1] "1.1 - 98.8 (12.1)" "0.1 - 84.7 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10P LOSS MUTATED"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-GN-A26D 
"10P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D57V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10P LOSS MUTATED                   11             1
  10P LOSS WILD-TYPE                 14             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10P LOSS MUTATED                                                                                         20
  10P LOSS WILD-TYPE                                                                                       15
                    vv
clus                 REGIONAL LYMPH NODE
  10P LOSS MUTATED                    45
  10P LOSS WILD-TYPE                  67
D57V3, multiclass
                                                                                          clus
vv                                                                                         10P LOSS MUTATED
  DISTANT METASTASIS                                                                                     11
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               20
  REGIONAL LYMPH NODE                                                                                    45
                                                                                          clus
vv                                                                                         10P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       14
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 15
  REGIONAL LYMPH NODE                                                                                      67
D57V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     36   41
  10P LOSS WILD-TYPE   31   65
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               36                 31
  MALE                 41                 65
                    vv
clus                 M0 M1 M1A M1B M1C
  10P LOSS MUTATED   68  0   1   1   2
  10P LOSS WILD-TYPE 82  2   1   1   0
D57V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10P LOSS MUTATED   44  0   5   6  0   0   6   4  7  0
  10P LOSS WILD-TYPE 51  2   2  10  1   4   5   1  9  2
D57V6, multiclass
D57V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10P LOSS MUTATED             4       7        5        7        9         2
  10P LOSS WILD-TYPE           0      10        5        7       10         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10P LOSS MUTATED           4         4         5          4          7
  10P LOSS WILD-TYPE         6         4         4          2         11
                    vv
clus                 STAGE IIIC STAGE IV
  10P LOSS MUTATED           10        4
  10P LOSS WILD-TYPE         13        2
D57V8, multiclass

Clustering(58) Variable = 10q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   15 27
  10Q LOSS WILD-TYPE 29 23
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                42                 52 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                 23 
$`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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       39.19        13.68         9.99        44.52        36.69        25.15 
TCGA-DA-A1IA TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        4.93        14.83         6.31         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29P TCGA-EE-A29X 
        8.81         4.41         1.08        27.12        12.03         8.09 
TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19L TCGA-ER-A3PL TCGA-FR-A3YN 
        9.67         8.94         3.52        12.99         1.71         5.95 
TCGA-FS-A1ZR TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
        8.81        24.85        31.33        10.09        16.21        12.16 

$`10Q LOSS WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CC 
       10.26         8.38        21.14        11.41        30.87        45.70 
TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I0 
       24.00         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-EE-A17X 
       22.36         6.64        19.36         7.00        17.56        11.57 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D 
        1.12         1.35        12.20         7.96        37.97        11.15 
TCGA-EE-A29E TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T 
       38.63         9.47         8.12         8.84         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-ER-A19F TCGA-ER-A19J 
        2.43        11.31        25.28        23.90        11.11         4.18 
TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A4F0 
       28.64        42.84        78.44         6.58        72.16        53.82 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A268 TCGA-GN-A26D 
       15.35        84.72        15.39        14.70 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.08               0.13 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             98.76              84.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            12.575             11.230 
[1] "1.1 - 98.8 (12.6)" "0.1 - 84.7 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-GN-A26D 
"10Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D58V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  10Q LOSS MUTATED                   12             1
  10Q LOSS WILD-TYPE                 13             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  10Q LOSS MUTATED                                                                                         22
  10Q LOSS WILD-TYPE                                                                                       13
                    vv
clus                 REGIONAL LYMPH NODE
  10Q LOSS MUTATED                    49
  10Q LOSS WILD-TYPE                  63
D58V3, multiclass
                                                                                          clus
vv                                                                                         10Q LOSS MUTATED
  DISTANT METASTASIS                                                                                     12
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               22
  REGIONAL LYMPH NODE                                                                                    49
                                                                                          clus
vv                                                                                         10Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       13
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 13
  REGIONAL LYMPH NODE                                                                                      63
D58V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     37   47
  10Q LOSS WILD-TYPE   30   59
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               37                 30
  MALE                 47                 59
                    vv
clus                 M0 M1 M1A M1B M1C
  10Q LOSS MUTATED   71  0   1   2   2
  10Q LOSS WILD-TYPE 79  2   1   0   0
D58V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  10Q LOSS MUTATED   48  0   4   6  0   1   6   4  7  0
  10Q LOSS WILD-TYPE 47  2   3  10  1   3   5   1  9  2
D58V6, multiclass
D58V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  10Q LOSS MUTATED             4       7        6        8        9         3
  10Q LOSS WILD-TYPE           0      10        4        6       10         5
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  10Q LOSS MUTATED           5         4         5          3          9
  10Q LOSS WILD-TYPE         5         4         4          3          9
                    vv
clus                 STAGE IIIC STAGE IV
  10Q LOSS MUTATED            8        4
  10Q LOSS WILD-TYPE         15        2
D58V8, multiclass

Clustering(59) Variable = 11p loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   14 18
  11P LOSS WILD-TYPE 30 32
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                 62 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                 32 
$`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-A1I5 TCGA-DA-A1I8 TCGA-EE-A182 
       48.79        35.80        39.19        44.52        25.15         1.35 
TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q TCGA-EE-A29R 
       37.97        11.15         1.08        27.12         8.12         8.84 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L 
        2.43         8.09        23.90         9.67         3.52        12.99 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 
        1.71         5.95        10.78         0.20        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
       30.87         6.35        15.25        45.70        13.32        24.00 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        5.39         4.01        51.12        10.03        13.68         9.99 
TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
       36.69         4.93        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-A20H TCGA-EE-A29A TCGA-EE-A29E 
        4.27        36.07         5.13         8.81         7.96        38.63 
TCGA-EE-A29H TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2A0 
        4.41         9.47        12.03         9.99         6.48        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       25.28         8.94        11.11         4.18        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
       78.44         6.58        72.16         8.81        53.82         3.22 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A265 TCGA-GN-A266 
        6.41         1.02         0.13        15.35        84.72        10.09 
TCGA-GN-A268 TCGA-GN-A26D 
       15.39        14.70 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.20               0.13 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             48.79              98.76 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            11.655             11.490 
[1] "0.2 - 48.8 (11.7)" "0.1 - 98.8 (11.5)"
        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-A2JF         TCGA-D3-A2JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED"   "11P LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-GN-A26D 
"11P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11P LOSS MUTATED                    7             1
  11P LOSS WILD-TYPE                 18             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11P LOSS MUTATED                                                                                         10
  11P LOSS WILD-TYPE                                                                                       25
                    vv
clus                 REGIONAL LYMPH NODE
  11P LOSS MUTATED                    27
  11P LOSS WILD-TYPE                  85
D59V3, multiclass
                                                                                          clus
vv                                                                                         11P LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               10
  REGIONAL LYMPH NODE                                                                                    27
                                                                                          clus
vv                                                                                         11P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 25
  REGIONAL LYMPH NODE                                                                                      85
D59V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     22   23
  11P LOSS WILD-TYPE   45   83
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               22                 45
  MALE                 23                 83
                    vv
clus                  M0  M1 M1A M1B M1C
  11P LOSS MUTATED    35   1   1   0   2
  11P LOSS WILD-TYPE 115   1   1   2   0
D59V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11P LOSS MUTATED   19  0   2   7  0   1   1   3  5  1
  11P LOSS WILD-TYPE 76  2   5   9  1   3  10   2 11  1
D59V6, multiclass
D59V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11P LOSS MUTATED             1       2        1        6        1         0
  11P LOSS WILD-TYPE           3      15        9        8       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11P LOSS MUTATED           3         2         1          2          6
  11P LOSS WILD-TYPE         7         6         8          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  11P LOSS MUTATED            9        4
  11P LOSS WILD-TYPE         14        2
D59V8, multiclass

Clustering(60) Variable = 11q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   14 17
  11Q LOSS WILD-TYPE 30 33
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                31                 63 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                17                 33 
$`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-A1I5 TCGA-DA-A1I8 
        2.86        48.79        35.80        39.19        44.52        25.15 
TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29Q 
        1.35        37.97        11.15         1.08        27.12         8.12 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A19D TCGA-ER-A19L 
        8.84         2.43        23.90         9.67         3.52        12.99 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FW-A3I3 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A26A 
        1.71         5.95         0.20        31.33        16.21        12.16 
TCGA-GN-A26D 
       14.70 

$`11Q LOSS WILD-TYPE`
TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JD TCGA-D3-A2JF 
       70.16        28.08         8.38        21.14        11.41        30.87 
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-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        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-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H 
       36.07         5.13         8.81         7.96        38.63         4.41 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.47        12.03         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
       25.28         8.94        11.11         4.18        28.64        42.84 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 
       78.44         6.58        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
       10.78         6.41         1.02         0.13        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 
              0.20               0.13 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             98.76              84.72 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             12.99              11.31 
[1] "0.2 - 98.8 (13.0)" "0.1 - 84.7 (11.3)"
        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-A2JF         TCGA-D3-A2JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"11Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "11Q LOSS MUTATED" 
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  11Q LOSS MUTATED                    9             1
  11Q LOSS WILD-TYPE                 16             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  11Q LOSS MUTATED                                                                                          9
  11Q LOSS WILD-TYPE                                                                                       26
                    vv
clus                 REGIONAL LYMPH NODE
  11Q LOSS MUTATED                    29
  11Q LOSS WILD-TYPE                  83
D60V3, multiclass
                                                                                          clus
vv                                                                                         11Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      9
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                9
  REGIONAL LYMPH NODE                                                                                    29
                                                                                          clus
vv                                                                                         11Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       16
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 26
  REGIONAL LYMPH NODE                                                                                      83
D60V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     23   25
  11Q LOSS WILD-TYPE   44   81
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               23                 44
  MALE                 25                 81
                    vv
clus                  M0  M1 M1A M1B M1C
  11Q LOSS MUTATED    38   1   1   0   2
  11Q LOSS WILD-TYPE 112   1   1   2   0
D60V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  11Q LOSS MUTATED   23  0   2   8  0   1   1   3  4  1
  11Q LOSS WILD-TYPE 72  2   5   8  1   3  10   2 12  1
D60V6, multiclass
D60V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  11Q LOSS MUTATED             1       2        1        7        1         0
  11Q LOSS WILD-TYPE           3      15        9        7       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  11Q LOSS MUTATED           4         4         1          2          6
  11Q LOSS WILD-TYPE         6         4         8          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  11Q LOSS MUTATED            9        4
  11Q LOSS WILD-TYPE         14        2
D60V8, multiclass

Clustering(61) Variable = 12p loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  1
  12P LOSS WILD-TYPE 40 49
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 89 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 49 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I2 
        2.86        48.79        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        5.13         8.81         7.96        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R 
        4.41         1.08        27.12         9.47        12.03         8.84 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        6.48         2.43         8.09        11.31        25.28         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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              8.12               0.13 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             39.19              98.76 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             10.26              11.57 
[1] "8.1 - 39.2 (10.3)" "0.1 - 98.8 (11.6)"
        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-A2JF         TCGA-D3-A2JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"12P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D61V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12P LOSS MUTATED                    2             0
  12P LOSS WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12P LOSS MUTATED                                                                                          3
  12P LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  12P LOSS MUTATED                     5
  12P LOSS WILD-TYPE                 107
D61V3, multiclass
                                                                                          clus
vv                                                                                         12P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         12P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     107
D61V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      5    5
  12P LOSS WILD-TYPE   62  101
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                5                 62
  MALE                  5                101
                    vv
clus                  M0  M1 M1A M1B M1C
  12P LOSS MUTATED     9   0   0   0   1
  12P LOSS WILD-TYPE 141   2   2   2   1
D61V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12P LOSS MUTATED    6  0   0   1  0   0   0   2  1  0
  12P LOSS WILD-TYPE 89  2   7  15  1   4  11   3 15  2
D61V6, multiclass
D61V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12P LOSS MUTATED             1       1        0        0        1         1
  12P LOSS WILD-TYPE           3      16       10       14       18         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12P LOSS MUTATED           2         0         0          0          2
  12P LOSS WILD-TYPE         8         8         9          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  12P LOSS MUTATED            1        1
  12P LOSS WILD-TYPE         22        5
D61V8, multiclass

Clustering(62) Variable = 12q loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    6  5
  12Q LOSS WILD-TYPE 38 45
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                 83 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                 45 
$`12Q LOSS MUTATED`
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-DA-A1I1 TCGA-EE-A29Q TCGA-EE-A29S 
       16.47        10.26        45.70        39.19         8.12         9.99 
TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-ER-A3PL TCGA-FS-A4F2 
        8.09        23.90         9.67         1.71         3.22 

$`12Q 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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CE 
       21.14        11.41        30.87         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-A1I5 
       35.80        51.12        10.03        13.68         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        7.96        37.97        11.15        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V 
       27.12         9.47        12.03         8.84         6.48         2.43 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J 
       11.31        25.28         8.94         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-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
       72.16         8.81        53.82        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        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 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1.71               0.13 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             45.70              98.76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              9.99              12.03 
[1] "1.7 - 45.7 (10.0)" "0.1 - 98.8 (12.0)"
        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 MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A2JD         TCGA-D3-A2JF         TCGA-D3-A2JK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "12Q LOSS MUTATED"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"12Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  12Q LOSS MUTATED                    3             0
  12Q LOSS WILD-TYPE                 22             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  12Q LOSS MUTATED                                                                                          7
  12Q LOSS WILD-TYPE                                                                                       28
                    vv
clus                 REGIONAL LYMPH NODE
  12Q LOSS MUTATED                     9
  12Q LOSS WILD-TYPE                 103
D62V3, multiclass
                                                                                          clus
vv                                                                                         12Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                7
  REGIONAL LYMPH NODE                                                                                     9
                                                                                          clus
vv                                                                                         12Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 28
  REGIONAL LYMPH NODE                                                                                     103
D62V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     10    9
  12Q LOSS WILD-TYPE   57   97
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               10                 57
  MALE                  9                 97
                    vv
clus                  M0  M1 M1A M1B M1C
  12Q LOSS MUTATED    16   0   1   0   1
  12Q LOSS WILD-TYPE 134   2   1   2   1
D62V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  12Q LOSS MUTATED   13  0   0   1  0   0   0   2  2  0
  12Q LOSS WILD-TYPE 82  2   7  15  1   4  11   3 14  2
D62V6, multiclass
D62V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  12Q LOSS MUTATED             1       1        1        2        2         1
  12Q LOSS WILD-TYPE           3      16        9       12       17         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  12Q LOSS MUTATED           2         2         0          0          2
  12Q LOSS WILD-TYPE         8         6         9          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  12Q LOSS MUTATED            2        2
  12Q LOSS WILD-TYPE         21        4
D62V8, multiclass

Clustering(63) Variable = 13q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    8  9
  13Q LOSS WILD-TYPE 36 41
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 77 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                 41 
$`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-A29M TCGA-EE-A29N 
        6.64         1.12        37.97        11.15        27.12         9.47 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-FR-A3YN TCGA-GN-A266 TCGA-GN-A26D 
        8.12         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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 
       35.80        51.12        10.03        39.19        44.52        36.69 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 
        4.93        22.36        19.36         7.00        17.56        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
       11.57         6.31         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13         8.81         7.96        38.63         4.41         1.08 
TCGA-EE-A29P TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 
       12.03         8.84         9.99         2.43         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-A4F2 TCGA-FS-A4F9 
        1.71        72.16         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
        6.41         0.20         1.02         0.13        15.35        24.85 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       31.33        84.72        16.21        15.39        12.16 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.12               0.13 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             48.79              98.76 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.09              12.03 
[1] "1.1 - 48.8 (10.1)" "0.1 - 98.8 (12.0)"
        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-A2JF         TCGA-D3-A2JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"13Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
  "13Q LOSS MUTATED" 
[1] "hr=" "1.2"
D63V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  13Q LOSS MUTATED                    1             1
  13Q LOSS WILD-TYPE                 24             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  13Q LOSS MUTATED                                                                                          6
  13Q LOSS WILD-TYPE                                                                                       29
                    vv
clus                 REGIONAL LYMPH NODE
  13Q LOSS MUTATED                    18
  13Q LOSS WILD-TYPE                  94
D63V3, multiclass
                                                                                          clus
vv                                                                                         13Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    18
                                                                                          clus
vv                                                                                         13Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      94
D63V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11   15
  13Q LOSS WILD-TYPE   56   91
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               11                 56
  MALE                 15                 91
                    vv
clus                  M0  M1 M1A M1B M1C
  13Q LOSS MUTATED    20   0   0   2   1
  13Q LOSS WILD-TYPE 130   2   2   0   1
D63V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  13Q LOSS MUTATED   11  0   0   3  0   0   3   3  3  1
  13Q LOSS WILD-TYPE 84  2   7  13  1   4   8   2 13  1
D63V6, multiclass
D63V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  13Q LOSS MUTATED             0       1        1        3        3         0
  13Q LOSS WILD-TYPE           4      16        9       11       16         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  13Q LOSS MUTATED           1         1         0          0          5
  13Q LOSS WILD-TYPE         9         7         9          6         13
                    vv
clus                 STAGE IIIC STAGE IV
  13Q LOSS MUTATED            3        2
  13Q LOSS WILD-TYPE         20        4
D63V8, multiclass

Clustering(64) Variable = 14q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   10 13
  14Q LOSS WILD-TYPE 34 37
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                23                 71 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 37 
$`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-A1I5 TCGA-DA-A3F5 TCGA-EE-A181 TCGA-EE-A29C TCGA-EE-A29V 
       39.19        44.52        17.56         1.12        37.97         2.43 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-ER-A3PL TCGA-FS-A1ZR TCGA-FS-A4F2 
        8.09         9.67         8.94         1.71         8.81         3.22 
TCGA-FS-A4F9 TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
       10.78        31.33        16.21        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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CF 
       21.14        11.41        30.87         6.35        15.25        24.00 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I0 
        9.30         5.39         4.01         2.86        35.80        10.03 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        36.69        25.15         4.93        22.36 
TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z 
        6.64        19.36         7.00        14.83        11.57         6.31 
TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.96        11.15        38.63         4.41         1.08        27.12 
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-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
       72.16        53.82         6.41         0.20         1.02         0.13 
TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26D 
       15.35        24.85        84.72        10.09        14.70 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.12               0.13 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             51.12              98.76 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.32              11.31 
[1] "1.1 - 51.1 (13.3)" "0.1 - 98.8 (11.3)"
        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-A2JF         TCGA-D3-A2JK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-GN-A26D 
"14Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  14Q LOSS MUTATED                    7             0
  14Q LOSS WILD-TYPE                 18             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  14Q LOSS MUTATED                                                                                         10
  14Q LOSS WILD-TYPE                                                                                       25
                    vv
clus                 REGIONAL LYMPH NODE
  14Q LOSS MUTATED                    25
  14Q LOSS WILD-TYPE                  87
D64V3, multiclass
                                                                                          clus
vv                                                                                         14Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               10
  REGIONAL LYMPH NODE                                                                                    25
                                                                                          clus
vv                                                                                         14Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 25
  REGIONAL LYMPH NODE                                                                                      87
D64V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     15   27
  14Q LOSS WILD-TYPE   52   79
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               15                 52
  MALE                 27                 79
                    vv
clus                  M0  M1 M1A M1B M1C
  14Q LOSS MUTATED    38   0   1   0   2
  14Q LOSS WILD-TYPE 112   2   1   2   0
D64V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  14Q LOSS MUTATED   25  0   3   4  0   0   1   3  5  0
  14Q LOSS WILD-TYPE 70  2   4  12  1   4  10   2 11  2
D64V6, multiclass
D64V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  14Q LOSS MUTATED             2       4        1        3        8         0
  14Q LOSS WILD-TYPE           2      13        9       11       11         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  14Q LOSS MUTATED           2         3         2          2          3
  14Q LOSS WILD-TYPE         8         5         7          4         15
                    vv
clus                 STAGE IIIC STAGE IV
  14Q LOSS MUTATED            7        3
  14Q LOSS WILD-TYPE         16        3
D64V8, multiclass

Clustering(65) Variable = 15q loss mutation analysis
D65V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    2  4
  15Q LOSS WILD-TYPE 42 46
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 88 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 4                 46 
$`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 

$`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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
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-A1I2 
        2.86        48.79        35.80        51.12        10.03        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        5.13         8.81         7.96        37.97        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
        4.41        27.12         9.47         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         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-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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 
        1.02         0.13        15.35        24.85        31.33        84.72 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       16.21        15.39        12.16        14.70 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.08               0.13 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             39.19              98.76 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             11.06              11.49 
[1] "1.1 - 39.2 (11.1)" "0.1 - 98.8 (11.5)"
        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-A2JF         TCGA-D3-A2JK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"15Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D65V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  15Q LOSS MUTATED                    1             0
  15Q LOSS WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  15Q LOSS MUTATED                                                                                          5
  15Q LOSS WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  15Q LOSS MUTATED                     5
  15Q LOSS WILD-TYPE                 107
D65V3, multiclass
                                                                                          clus
vv                                                                                         15Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     5
                                                                                          clus
vv                                                                                         15Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     107
D65V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    6
  15Q LOSS WILD-TYPE   62  100
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                5                 62
  MALE                  6                100
                    vv
clus                  M0  M1 M1A M1B M1C
  15Q LOSS MUTATED     9   0   0   1   0
  15Q LOSS WILD-TYPE 141   2   2   1   2
D65V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  15Q LOSS MUTATED    6  0   0   0  0   0   0   1  3  0
  15Q LOSS WILD-TYPE 89  2   7  16  1   4  11   4 13  2
D65V6, multiclass
D65V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  15Q LOSS MUTATED             0       1        1        2        1         0
  15Q LOSS WILD-TYPE           4      16        9       12       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  15Q LOSS MUTATED           0         1         1          0          0
  15Q LOSS WILD-TYPE        10         7         8          6         18
                    vv
clus                 STAGE IIIC STAGE IV
  15Q LOSS MUTATED            2        0
  15Q LOSS WILD-TYPE         21        6
D65V8, multiclass

Clustering(66) Variable = 16p loss mutation analysis
D66V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    2  9
  16P LOSS WILD-TYPE 42 41
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                 83 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                 41 
$`16P LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-EE-A17Z TCGA-EE-A29D 
       32.55        22.55        35.80        13.68         6.31        11.15 
TCGA-EE-A29X TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
        8.09         0.13        24.85        31.33        15.39 

$`16P LOSS 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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       21.14        11.41        30.87         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-A1I5 
       48.79        51.12        10.03        39.19         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       36.69        25.15         4.93        22.36         6.64        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
        7.00        17.56        14.83        11.57         1.12         1.35 
TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A 
       12.20         4.27        36.07         5.13         8.81         7.96 
TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       37.97        38.63         4.41         1.08        27.12         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V 
       12.03         8.12         8.84         9.99         6.48         2.43 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 
        3.22        10.78         6.41         0.20         1.02        15.35 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        10.09        16.21        12.16        14.70 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.13               0.20 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.80              98.76 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             15.39              11.31 
[1] "0.1 - 35.8 (15.4)" "0.2 - 98.8 (11.3)"
        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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16P LOSS MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"16P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D66V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16P LOSS MUTATED                    2             0
  16P LOSS WILD-TYPE                 23             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16P LOSS MUTATED                                                                                          1
  16P LOSS WILD-TYPE                                                                                       34
                    vv
clus                 REGIONAL LYMPH NODE
  16P LOSS MUTATED                    11
  16P LOSS WILD-TYPE                 101
D66V3, multiclass
                                                                                          clus
vv                                                                                         16P LOSS MUTATED
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                    11
                                                                                          clus
vv                                                                                         16P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       23
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 34
  REGIONAL LYMPH NODE                                                                                     101
D66V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    7
  16P LOSS WILD-TYPE   60   99
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                 60
  MALE                  7                 99
                    vv
clus                  M0  M1 M1A M1B M1C
  16P LOSS MUTATED    11   0   0   0   0
  16P LOSS WILD-TYPE 139   2   2   2   2
D66V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16P LOSS MUTATED    7  0   0   2  0   1   1   0  0  0
  16P LOSS WILD-TYPE 88  2   7  14  1   3  10   5 16  2
D66V6, multiclass
D66V7, 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           3      17       10       13       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16P LOSS MUTATED           3         1         0          0          2
  16P LOSS WILD-TYPE         7         7         9          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  16P LOSS MUTATED            2        0
  16P LOSS WILD-TYPE         21        6
D66V8, multiclass

Clustering(67) Variable = 16q loss mutation analysis
D67V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    6 14
  16Q LOSS WILD-TYPE 38 36
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 74 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                 36 
$`16Q LOSS MUTATED`
TCGA-D3-A1Q5 TCGA-D3-A1Q9 TCGA-D3-A2JF TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1I2 
       32.55        22.55        30.87         2.86        35.80        13.68 
TCGA-DA-A1I4 TCGA-DA-A3F8 TCGA-EE-A17Z TCGA-EE-A185 TCGA-EE-A29D TCGA-EE-A29X 
        9.99        14.83         6.31         4.27        11.15         8.09 
TCGA-EE-A2A5 TCGA-FS-A4F2 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A264 
        9.67         3.22         0.20         0.13        24.85        31.33 
TCGA-GN-A267 TCGA-GN-A268 
       16.21        15.39 

$`16Q LOSS 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-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-A1HV TCGA-DA-A1HY 
       24.00         9.30         5.39         4.01        48.79        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       10.03        39.19        44.52        36.69        25.15         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A17X 
       22.36         6.64        19.36         7.00        17.56        11.57 
TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.12         1.35        12.20        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        7.96        37.97        38.63         4.41         1.08        27.12 
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-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-ER-A19D 
        2.43        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-A265 TCGA-GN-A266 
       10.78         6.41         1.02        15.35        84.72        10.09 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.13               1.02 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.80              98.76 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            12.415             11.490 
[1] "0.1 - 35.8 (12.4)" "1.0 - 98.8 (11.5)"
        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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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 MUTATED" 
        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-A2JF         TCGA-D3-A2JK 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D67V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  16Q LOSS MUTATED                    7             0
  16Q LOSS WILD-TYPE                 18             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  16Q LOSS MUTATED                                                                                          5
  16Q LOSS WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  16Q LOSS MUTATED                    19
  16Q LOSS WILD-TYPE                  93
D67V3, multiclass
                                                                                          clus
vv                                                                                         16Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    19
                                                                                          clus
vv                                                                                         16Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      93
D67V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     13   18
  16Q LOSS WILD-TYPE   54   88
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               13                 54
  MALE                 18                 88
                    vv
clus                  M0  M1 M1A M1B M1C
  16Q LOSS MUTATED    25   1   0   1   0
  16Q LOSS WILD-TYPE 125   1   2   1   2
D67V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  16Q LOSS MUTATED   15  0   2   4  0   1   3   0  2  0
  16Q LOSS WILD-TYPE 80  2   5  12  1   3   8   5 14  2
D67V6, multiclass
D67V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  16Q LOSS MUTATED             1       0        1        2        4         0
  16Q LOSS WILD-TYPE           3      17        9       12       15         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  16Q LOSS MUTATED           3         3         0          1          6
  16Q LOSS WILD-TYPE         7         5         9          5         12
                    vv
clus                 STAGE IIIC STAGE IV
  16Q LOSS MUTATED            3        1
  16Q LOSS WILD-TYPE         20        5
D67V8, multiclass

Clustering(68) Variable = 17p loss mutation analysis
D68V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   13 10
  17P LOSS WILD-TYPE 31 40
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                23                 71 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 40 
$`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-A29M TCGA-EE-A29S TCGA-EE-A29T 
        4.27        37.97         4.41        27.12         9.99         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-FR-A3YN 
        2.43         8.09        25.28        23.90         9.67         5.95 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A266 
        3.22        10.78         0.20         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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         6.35        15.25 
TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 
       45.70        13.32        24.00         5.39         4.01         2.86 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F5 
       25.15         4.93        22.36         6.64        19.36        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E 
       36.07         5.13         8.81         7.96        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A2A0 
        1.08         9.47        12.03         8.12         8.84        11.31 
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-A44A TCGA-FS-A1ZR 
       42.84        78.44         6.58         1.71        72.16         8.81 
TCGA-FS-A4F0 TCGA-FS-A4FC TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       53.82         6.41         0.13        15.35        24.85        31.33 
TCGA-GN-A265 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A TCGA-GN-A26D 
       84.72        16.21        15.39        12.16        14.70 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.20               0.13 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             51.12              98.76 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.67              12.99 
[1] "0.2 - 51.1 (9.7)"  "0.1 - 98.8 (13.0)"
        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-A2JF         TCGA-D3-A2JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17P LOSS MUTATED                    5             1
  17P LOSS WILD-TYPE                 20             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17P LOSS MUTATED                                                                                          5
  17P LOSS WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  17P LOSS MUTATED                    27
  17P LOSS WILD-TYPE                  85
D68V3, multiclass
                                                                                          clus
vv                                                                                         17P LOSS MUTATED
  DISTANT METASTASIS                                                                                      5
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                    27
                                                                                          clus
vv                                                                                         17P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       20
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                      85
D68V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     13   25
  17P LOSS WILD-TYPE   54   81
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               13                 54
  MALE                 25                 81
                    vv
clus                  M0  M1 M1A M1B M1C
  17P LOSS MUTATED    34   1   0   1   1
  17P LOSS WILD-TYPE 116   1   2   1   1
D68V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17P LOSS MUTATED   22  0   1   3  1   1   2   2  4  1
  17P LOSS WILD-TYPE 73  2   6  13  0   3   9   3 12  1
D68V6, multiclass
D68V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17P LOSS MUTATED             1       4        3        6        1         2
  17P LOSS WILD-TYPE           3      13        7        8       18         6
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17P LOSS MUTATED           3         1         2          1          5
  17P LOSS WILD-TYPE         7         7         7          5         13
                    vv
clus                 STAGE IIIC STAGE IV
  17P LOSS MUTATED            4        2
  17P LOSS WILD-TYPE         19        4
D68V8, multiclass

Clustering(69) Variable = 17q loss mutation analysis
D69V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    4  6
  17Q LOSS WILD-TYPE 40 44
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                10                 84 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 6                 44 
$`17Q LOSS MUTATED`
TCGA-D3-A2J6 TCGA-DA-A1HW TCGA-EE-A29C TCGA-EE-A29X TCGA-EE-A2A5 TCGA-ER-A19L 
       10.26        35.80        37.97         8.09         9.67        12.99 
TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 
        3.22        10.78         0.20         1.02 

$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 
        2.86        48.79        51.12        10.03        39.19        13.68 
TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB 
        9.99        44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        5.13         8.81         7.96        11.15        38.63         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        9.99         6.48         2.43        11.31        25.28        23.90 
TCGA-EE-A2A6 TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19N 
        8.94         3.52        11.11         4.18        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-A4FC TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
       53.82         6.41         0.13        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 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.20               0.13 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             37.97              98.76 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             9.965             12.095 
[1] "0.2 - 38.0 (10.0)" "0.1 - 98.8 (12.1)"
        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-A2JF         TCGA-D3-A2JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED"   "17Q LOSS MUTATED" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"17Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D69V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  17Q LOSS MUTATED                    3             0
  17Q LOSS WILD-TYPE                 22             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  17Q LOSS MUTATED                                                                                          2
  17Q LOSS WILD-TYPE                                                                                       33
                    vv
clus                 REGIONAL LYMPH NODE
  17Q LOSS MUTATED                    12
  17Q LOSS WILD-TYPE                 100
D69V3, multiclass
                                                                                          clus
vv                                                                                         17Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         17Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     100
D69V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      6   11
  17Q LOSS WILD-TYPE   61   95
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                6                 61
  MALE                 11                 95
                    vv
clus                  M0  M1 M1A M1B M1C
  17Q LOSS MUTATED    14   1   0   0   1
  17Q LOSS WILD-TYPE 136   1   2   2   1
D69V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  17Q LOSS MUTATED   10  0   1   1  1   1   0   1  1  0
  17Q LOSS WILD-TYPE 85  2   6  15  0   3  11   4 15  2
D69V6, multiclass
D69V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  17Q LOSS MUTATED             1       1        1        3        0         1
  17Q LOSS WILD-TYPE           3      16        9       11       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  17Q LOSS MUTATED           1         1         1          1          2
  17Q LOSS WILD-TYPE         9         7         8          5         16
                    vv
clus                 STAGE IIIC STAGE IV
  17Q LOSS MUTATED            1        2
  17Q LOSS WILD-TYPE         22        4
D69V8, multiclass

Clustering(70) Variable = 18p loss mutation analysis
D70V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    7  9
  18P LOSS WILD-TYPE 37 41
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                 78 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 41 
$`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-A29A TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T 
       17.56        36.07         7.96        11.15        27.12         6.48 
TCGA-EE-A29V TCGA-EE-A29X TCGA-FS-A1ZR TCGA-FW-A3TU 
        2.43         8.09         8.81         0.13 

$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CE 
       21.14        11.41        30.87         6.35        45.70        13.32 
TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW 
       24.00         9.30         5.39         4.01         2.86        35.80 
TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 
       51.12        10.03        39.19         9.99        44.52        25.15 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 
        4.93        22.36         6.64        19.36         7.00        14.83 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A185 
       11.57         6.31         1.12         1.35        12.20         4.27 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        5.13         8.81        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-A2A0 
        9.47        12.03         8.12         8.84         9.99        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-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
        1.71         5.95        72.16        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 
        6.41         0.20         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 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.20 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             70.16              98.76 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            14.465             11.360 
[1] "0.1 - 70.2 (14.5)" "0.2 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"18P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D70V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18P LOSS MUTATED                    7             1
  18P LOSS WILD-TYPE                 18             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18P LOSS MUTATED                                                                                          8
  18P LOSS WILD-TYPE                                                                                       27
                    vv
clus                 REGIONAL LYMPH NODE
  18P LOSS MUTATED                    19
  18P LOSS WILD-TYPE                  93
D70V3, multiclass
                                                                                          clus
vv                                                                                         18P LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                8
  REGIONAL LYMPH NODE                                                                                    19
                                                                                          clus
vv                                                                                         18P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 27
  REGIONAL LYMPH NODE                                                                                      93
D70V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15   20
  18P LOSS WILD-TYPE   52   86
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               15                 52
  MALE                 20                 86
                    vv
clus                  M0  M1 M1A M1B M1C
  18P LOSS MUTATED    32   0   0   0   0
  18P LOSS WILD-TYPE 118   2   2   2   2
D70V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18P LOSS MUTATED   16  0   3   3  0   1   3   2  2  2
  18P LOSS WILD-TYPE 79  2   4  13  1   3   8   3 14  0
D70V6, multiclass
D70V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18P LOSS MUTATED             2       1        2        3        7         0
  18P LOSS WILD-TYPE           2      16        8       11       12         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18P LOSS MUTATED           1         0         2          2          5
  18P LOSS WILD-TYPE         9         8         7          4         13
                    vv
clus                 STAGE IIIC STAGE IV
  18P LOSS MUTATED            5        0
  18P LOSS WILD-TYPE         18        6
D70V8, multiclass

Clustering(71) Variable = 18q loss mutation analysis
D71V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    7 11
  18Q LOSS WILD-TYPE 37 39
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                 76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 39 
$`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-A1IA TCGA-DA-A3F5 TCGA-EE-A20B TCGA-EE-A29A 
       13.68        36.69         4.93        17.56        36.07         7.96 
TCGA-EE-A29D TCGA-EE-A29M TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-FW-A3TU 
       11.15        27.12         6.48         2.43         8.09         0.13 

$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3MO 
       11.41        30.87         6.35        45.70        24.00         9.30 
TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 
        5.39         4.01         2.86        35.80        51.12        10.03 
TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I8 TCGA-DA-A1IB TCGA-DA-A1IC 
       39.19         9.99        44.52        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29C 
        1.35        12.20         4.27         5.13         8.81        37.97 
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-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 
        8.84         9.99        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 
        8.81        53.82         3.22        10.78         6.41         0.20 
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 
              0.13               0.20 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             70.16              98.76 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            14.465             11.210 
[1] "0.1 - 70.2 (14.5)" "0.2 - 98.8 (11.2)"
        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-A2JF         TCGA-D3-A2JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "18Q LOSS MUTATED" "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-A182         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "18Q LOSS MUTATED" "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-A182         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
  "18Q LOSS MUTATED" "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-A182         TCGA-EE-A183 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "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-A29M         TCGA-EE-A29N 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"18Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  18Q LOSS MUTATED                    7             1
  18Q LOSS WILD-TYPE                 18             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  18Q LOSS MUTATED                                                                                          6
  18Q LOSS WILD-TYPE                                                                                       29
                    vv
clus                 REGIONAL LYMPH NODE
  18Q LOSS MUTATED                    19
  18Q LOSS WILD-TYPE                  93
D71V3, multiclass
                                                                                          clus
vv                                                                                         18Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      7
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                6
  REGIONAL LYMPH NODE                                                                                    19
                                                                                          clus
vv                                                                                         18Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       18
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 29
  REGIONAL LYMPH NODE                                                                                      93
D71V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     14   19
  18Q LOSS WILD-TYPE   53   87
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               14                 53
  MALE                 19                 87
                    vv
clus                  M0  M1 M1A M1B M1C
  18Q LOSS MUTATED    30   0   0   1   0
  18Q LOSS WILD-TYPE 120   2   2   1   2
D71V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  18Q LOSS MUTATED   13  0   3   5  0   2   3   1  3  1
  18Q LOSS WILD-TYPE 82  2   4  11  1   2   8   4 13  1
D71V6, multiclass
D71V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  18Q LOSS MUTATED             2       0        2        3        5         0
  18Q LOSS WILD-TYPE           2      17        8       11       14         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  18Q LOSS MUTATED           1         0         3          2          6
  18Q LOSS WILD-TYPE         9         8         6          4         12
                    vv
clus                 STAGE IIIC STAGE IV
  18Q LOSS MUTATED            5        0
  18Q LOSS WILD-TYPE         18        6
D71V8, multiclass

Clustering(72) Variable = 19p loss mutation analysis
D72V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    3  6
  19P LOSS WILD-TYPE 41 44
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 9                 85 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 6                 44 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC 
       21.14        11.41        30.87         6.35        15.25        45.70 
TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1HY 
       13.32        24.00         9.30         5.39         4.01        51.12 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
       10.03        39.19        13.68         9.99        44.52        36.69 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F5 
        4.93        22.36         6.64        19.36         7.00        17.56 
TCGA-DA-A3F8 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
       14.83        11.57         6.31         1.12         1.35        12.20 
TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        4.27        36.07         5.13         8.81         7.96        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
       11.15        38.63         1.08        27.12         9.47        12.03 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A1 
        8.12         8.84         9.99         6.48         2.43        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-A4F2 TCGA-FS-A4F9 
        5.95        72.16         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 
        6.41         0.20         1.02         0.13        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 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.86               0.13 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             48.79              98.76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             16.47              11.41 
[1] "2.9 - 48.8 (16.5)" "0.1 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED"   "19P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19P LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19P LOSS MUTATED"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"19P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19P LOSS MUTATED                    1             0
  19P LOSS WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19P LOSS MUTATED                                                                                          2
  19P LOSS WILD-TYPE                                                                                       33
                    vv
clus                 REGIONAL LYMPH NODE
  19P LOSS MUTATED                    12
  19P LOSS WILD-TYPE                 100
D72V3, multiclass
                                                                                          clus
vv                                                                                         19P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 33
  REGIONAL LYMPH NODE                                                                                     100
D72V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10    5
  19P LOSS WILD-TYPE   57  101
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                 57
  MALE                  5                101
                    vv
clus                  M0  M1 M1A M1B M1C
  19P LOSS MUTATED    13   0   0   1   1
  19P LOSS WILD-TYPE 137   2   2   1   1
D72V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19P LOSS MUTATED    5  0   1   2  0   1   2   1  3  0
  19P LOSS WILD-TYPE 90  2   6  14  1   3   9   4 13  2
D72V6, multiclass
D72V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19P LOSS MUTATED             1       0        1        1        0         1
  19P LOSS WILD-TYPE           3      17        9       13       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19P LOSS MUTATED           0         1         1          0          5
  19P LOSS WILD-TYPE        10         7         8          6         13
                    vv
clus                 STAGE IIIC STAGE IV
  19P LOSS MUTATED            2        1
  19P LOSS WILD-TYPE         21        5
D72V8, multiclass

Clustering(73) Variable = 19q loss mutation analysis
D73V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    6  4
  19Q LOSS WILD-TYPE 38 46
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                 84 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 46 
$`19Q LOSS MUTATED`
TCGA-D3-A1Q9 TCGA-D9-A3Z3 TCGA-DA-A1HV TCGA-DA-A1I8 TCGA-EE-A29H TCGA-EE-A29M 
       22.55         2.86        48.79        25.15         4.41        27.12 
TCGA-EE-A29S TCGA-EE-A29X TCGA-GN-A26A TCGA-GN-A26D 
        9.99         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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 
       44.52        36.69         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F TCGA-EE-A20H 
        1.35        12.20         4.27        36.07         5.13         8.81 
TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29N 
        7.96        37.97        11.15        38.63         1.08         9.47 
TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
       12.03         8.12         8.84         6.48         2.43        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-A4F2 
        1.71         5.95        72.16         8.81        53.82         3.22 
TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 
       10.78         6.41         0.20         1.02         0.13        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 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2.86               0.13 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             48.79              98.76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             13.43              11.36 
[1] "2.9 - 48.8 (13.4)" "0.1 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "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-A2JF         TCGA-D3-A2JK 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED"   "19Q LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-DA-A1IA         TCGA-DA-A1IB         TCGA-DA-A1IC 
"19Q LOSS WILD-TYPE" "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-A182         TCGA-EE-A183 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
  "19Q LOSS MUTATED" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE"   "19Q LOSS MUTATED" 
        TCGA-GN-A26D 
  "19Q LOSS MUTATED" 
[1] "hr=" "1.4"
D73V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  19Q LOSS MUTATED                    0             1
  19Q LOSS WILD-TYPE                 25             0
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  19Q LOSS MUTATED                                                                                          3
  19Q LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  19Q LOSS MUTATED                    12
  19Q LOSS WILD-TYPE                 100
D73V3, multiclass
                                                                                          clus
vv                                                                                         19Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      0
  PRIMARY TUMOR                                                                                           1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    12
                                                                                          clus
vv                                                                                         19Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       25
  PRIMARY TUMOR                                                                                             0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     100
D73V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      9    7
  19Q LOSS WILD-TYPE   58   99
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                9                 58
  MALE                  7                 99
                    vv
clus                  M0  M1 M1A M1B M1C
  19Q LOSS MUTATED    11   0   0   1   1
  19Q LOSS WILD-TYPE 139   2   2   1   1
D73V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  19Q LOSS MUTATED    5  0   2   1  0   1   2   1  2  0
  19Q LOSS WILD-TYPE 90  2   5  15  1   3   9   4 14  2
D73V6, multiclass
D73V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  19Q LOSS MUTATED             0       0        1        2        0         1
  19Q LOSS WILD-TYPE           4      17        9       12       19         7
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  19Q LOSS MUTATED           0         1         1          1          4
  19Q LOSS WILD-TYPE        10         7         8          5         14
                    vv
clus                 STAGE IIIC STAGE IV
  19Q LOSS MUTATED            1        1
  19Q LOSS WILD-TYPE         22        5
D73V8, multiclass

Clustering(74) Variable = 20p loss mutation analysis
D74V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  2
  20P LOSS WILD-TYPE 40 48
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 88 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 48 
$`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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D9-A3Z1 
       15.25        45.70        13.32         9.30         5.39         4.01 
TCGA-D9-A3Z3 TCGA-DA-A1HW TCGA-DA-A1HY TCGA-DA-A1I0 TCGA-DA-A1I2 TCGA-DA-A1I4 
        2.86        35.80        51.12        10.03        13.68         9.99 
TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
        8.81         7.96        37.97        11.15         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         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-FR-A3YN TCGA-FR-A44A 
       28.64        42.84        78.44         6.58         5.95        72.16 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 
        0.13        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 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.71               0.13 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             48.79              98.76 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            31.315             11.360 
[1] "1.7 - 48.8 (31.3)" "0.1 - 98.8 (11.4)"
        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-A2JF         TCGA-D3-A2JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"20P LOSS WILD-TYPE" 
[1] "hr=" "2.4"
D74V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  20P LOSS MUTATED                    1             0
  20P LOSS WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  20P LOSS MUTATED                                                                                          3
  20P LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  20P LOSS MUTATED                     3
  20P LOSS WILD-TYPE                 109
D74V3, multiclass
                                                                                          clus
vv                                                                                         20P LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                     3
                                                                                          clus
vv                                                                                         20P LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                     109
D74V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2    5
  20P LOSS WILD-TYPE   65  101
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                2                 65
  MALE                  5                101
                    vv
clus                  M0  M1 M1A M1B M1C
  20P LOSS MUTATED     6   0   1   0   0
  20P LOSS WILD-TYPE 144   2   1   2   2
D74V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  20P LOSS MUTATED    3  0   0   1  0   0   1   0  2  0
  20P LOSS WILD-TYPE 92  2   7  15  1   4  10   5 14  2
D74V6, multiclass
D74V7, 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           4      17       10       14       18         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  20P LOSS MUTATED           0         1         0          0          2
  20P LOSS WILD-TYPE        10         7         9          6         16
                    vv
clus                 STAGE IIIC STAGE IV
  20P LOSS MUTATED            2        1
  20P LOSS WILD-TYPE         21        5
D74V8, multiclass

Clustering(75) Variable = 21q loss mutation analysis
D75V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    4  4
  21Q LOSS WILD-TYPE 40 46
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 86 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 4                 46 
$`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-A2JF TCGA-D3-A2JK TCGA-D3-A3C6 
        8.38        21.14        11.41        30.87         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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA 
       13.68         9.99        44.52        36.69        25.15         4.93 
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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20F 
       11.57         6.31         1.35        12.20         4.27         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L 
        8.81         7.96        37.97        11.15        38.63         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 
        6.48         2.43         8.09        11.31        25.28         9.67 
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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 
       53.82         3.22        10.78         6.41         0.20         1.02 
TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A267 
        0.13        15.35        24.85        31.33        84.72        16.21 
TCGA-GN-A26A TCGA-GN-A26D 
       12.16        14.70 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.12               0.13 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             36.07              98.76 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             12.74              11.49 
[1] "1.1 - 36.1 (12.7)" "0.1 - 98.8 (11.5)"
        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-A2JF         TCGA-D3-A2JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         TCGA-EE-A29C 
"21Q LOSS WILD-TYPE" "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-A29M         TCGA-EE-A29N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"21Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D75V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  21Q LOSS MUTATED                    3             0
  21Q LOSS WILD-TYPE                 22             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  21Q LOSS MUTATED                                                                                          3
  21Q LOSS WILD-TYPE                                                                                       32
                    vv
clus                 REGIONAL LYMPH NODE
  21Q LOSS MUTATED                    15
  21Q LOSS WILD-TYPE                  97
D75V3, multiclass
                                                                                          clus
vv                                                                                         21Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      3
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                3
  REGIONAL LYMPH NODE                                                                                    15
                                                                                          clus
vv                                                                                         21Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       22
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 32
  REGIONAL LYMPH NODE                                                                                      97
D75V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      9   12
  21Q LOSS WILD-TYPE   58   94
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                9                 58
  MALE                 12                 94
                    vv
clus                  M0  M1 M1A M1B M1C
  21Q LOSS MUTATED    20   0   0   0   0
  21Q LOSS WILD-TYPE 130   2   2   2   2
D75V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  21Q LOSS MUTATED   16  0   1   1  0   0   1   1  0  0
  21Q LOSS WILD-TYPE 79  2   6  15  1   4  10   4 16  2
D75V6, multiclass
D75V7, 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           3      15        7       14       13         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  21Q LOSS MUTATED           2         2         0          1          2
  21Q LOSS WILD-TYPE         8         6         9          5         16
                    vv
clus                 STAGE IIIC STAGE IV
  21Q LOSS MUTATED            1        0
  21Q LOSS WILD-TYPE         22        6
D75V8, multiclass

Clustering(76) Variable = 22q loss mutation analysis
D76V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    4  3
  22Q LOSS WILD-TYPE 40 47
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                 87 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 47 
$`22Q LOSS MUTATED`
TCGA-D3-A1Q8 TCGA-D3-A2JF TCGA-DA-A1I2 TCGA-EE-A29C TCGA-EE-A2A6 TCGA-ER-A19D 
       28.08        30.87        13.68        37.97         8.94         3.52 
TCGA-FS-A4F0 
       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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC 
       44.52        36.69        25.15         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20F 
        1.12         1.35        12.20         4.27        36.07         5.13 
TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L 
        8.81         7.96        11.15        38.63         4.41         1.08 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S 
       27.12         9.47        12.03         8.12         8.84         9.99 
TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 
        6.48         2.43         8.09        11.31        25.28        23.90 
TCGA-EE-A2A5 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19N 
        9.67        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-A4F2 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
        3.22        10.78         6.41         0.20         1.02         0.13 
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 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              3.52               0.13 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             53.82              98.76 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             28.08              11.31 
[1] "3.5 - 53.8 (28.1)" "0.1 - 98.8 (11.3)"
        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-A2JF         TCGA-D3-A2JK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"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-A2JF         TCGA-D3-A2JK 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3C6         TCGA-D3-A3CC         TCGA-D3-A3CE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D3-A3CF         TCGA-D3-A3MO         TCGA-D3-A3MV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-D9-A3Z1         TCGA-D9-A3Z3         TCGA-DA-A1HV 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1HW         TCGA-DA-A1HY         TCGA-DA-A1I0 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I1         TCGA-DA-A1I2         TCGA-DA-A1I4 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1I5         TCGA-DA-A1I7         TCGA-DA-A1I8 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DA-A1IA         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-A182         TCGA-EE-A183 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A185         TCGA-EE-A20B         TCGA-EE-A20F 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A20H         TCGA-EE-A29A         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-A29M         TCGA-EE-A29N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29P         TCGA-EE-A29Q         TCGA-EE-A29R 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29S         TCGA-EE-A29T         TCGA-EE-A29V 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A29X         TCGA-EE-A2A0         TCGA-EE-A2A1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EE-A2A2         TCGA-EE-A2A5         TCGA-EE-A2A6 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-ER-A19D         TCGA-ER-A19F         TCGA-ER-A19J 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A19M         TCGA-ER-A19N 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ER-A1A1         TCGA-ER-A3ET         TCGA-ER-A3PL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FR-A3YN         TCGA-FR-A44A         TCGA-FS-A1ZR 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4F0         TCGA-FS-A4F2         TCGA-FS-A4F9 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FS-A4FC         TCGA-FW-A3I3         TCGA-FW-A3R5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FW-A3TU         TCGA-GN-A261         TCGA-GN-A262 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A264         TCGA-GN-A265         TCGA-GN-A266 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A267         TCGA-GN-A268         TCGA-GN-A26A 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-GN-A26D 
"22Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D76V2, continuous
                    vv
clus                 DISTANT METASTASIS PRIMARY TUMOR
  22Q LOSS MUTATED                    1             0
  22Q LOSS WILD-TYPE                 24             1
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  22Q LOSS MUTATED                                                                                          5
  22Q LOSS WILD-TYPE                                                                                       30
                    vv
clus                 REGIONAL LYMPH NODE
  22Q LOSS MUTATED                     7
  22Q LOSS WILD-TYPE                 105
D76V3, multiclass
                                                                                          clus
vv                                                                                         22Q LOSS MUTATED
  DISTANT METASTASIS                                                                                      1
  PRIMARY TUMOR                                                                                           0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                5
  REGIONAL LYMPH NODE                                                                                     7
                                                                                          clus
vv                                                                                         22Q LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                       24
  PRIMARY TUMOR                                                                                             1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 30
  REGIONAL LYMPH NODE                                                                                     105
D76V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    7
  22Q LOSS WILD-TYPE   61   99
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 61
  MALE                  7                 99
                    vv
clus                  M0  M1 M1A M1B M1C
  22Q LOSS MUTATED    12   0   0   1   0
  22Q LOSS WILD-TYPE 138   2   2   1   2
D76V5, multiclass
                    vv
clus                 N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  22Q LOSS MUTATED    9  0   1   1  0   0   1   0  1  0
  22Q LOSS WILD-TYPE 86  2   6  15  1   4  10   5 15  2
D76V6, multiclass
D76V7, continuous
                    vv
clus                 I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  22Q LOSS MUTATED             0       3        2        3        0         0
  22Q LOSS WILD-TYPE           4      14        8       11       19         8
                    vv
clus                 STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  22Q LOSS MUTATED           1         0         0          0          1
  22Q LOSS WILD-TYPE         9         8         9          6         17
                    vv
clus                 STAGE IIIC STAGE IV
  22Q LOSS MUTATED            1        1
  22Q LOSS WILD-TYPE         22        5
D76V8, multiclass

Clustering(77) Variable = Xq loss mutation analysis
D77V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    2  2
  XQ LOSS WILD-TYPE 42 48
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                90 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                48 
$`XQ LOSS MUTATED`
TCGA-D3-A3C6 TCGA-DA-A1I8 TCGA-EE-A29H TCGA-GN-A262 
       15.25        25.15         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-A2JF TCGA-D3-A2JK 
       10.26         8.38        21.14        11.41        30.87         6.35 
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-A1I5 TCGA-DA-A1I7 TCGA-DA-A1IA TCGA-DA-A1IB 
       13.68         9.99        44.52        36.69         4.93        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-A182 TCGA-EE-A183 TCGA-EE-A185 TCGA-EE-A20B 
        6.31         1.12         1.35        12.20         4.27        36.07 
TCGA-EE-A20F TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        5.13         8.81         7.96        37.97        11.15        38.63 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29R 
        1.08        27.12         9.47        12.03         8.12         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 
        9.99         6.48         2.43         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-FR-A44A TCGA-FS-A1ZR TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F9 
        5.95        72.16         8.81        53.82         3.22        10.78 
TCGA-FS-A4FC TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-GN-A261 TCGA-GN-A264 
        6.41         0.20         1.02         0.13        15.35        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 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             4.41              0.13 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            25.15             98.76 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            20.05             11.36 
[1] "4.4 - 25.1 (20.1)" "0.1 - 98.8 (11.4)"
       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-A2JF        TCGA-D3-A2JK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"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-A2JF        TCGA-D3-A2JK 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3C6        TCGA-D3-A3CC        TCGA-D3-A3CE        TCGA-D3-A3CF 
  "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-D3-A3MO        TCGA-D3-A3MV        TCGA-D9-A3Z1        TCGA-D9-A3Z3 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1HV        TCGA-DA-A1HW        TCGA-DA-A1HY        TCGA-DA-A1I0 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I1        TCGA-DA-A1I2        TCGA-DA-A1I4        TCGA-DA-A1I5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1I7        TCGA-DA-A1I8        TCGA-DA-A1IA        TCGA-DA-A1IB 
"XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A1IC        TCGA-DA-A3F2        TCGA-DA-A3F3        TCGA-DA-A3F5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DA-A3F8        TCGA-EE-A17X        TCGA-EE-A17Z        TCGA-EE-A181 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A182        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-A20H        TCGA-EE-A29A        TCGA-EE-A29C 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29D        TCGA-EE-A29E        TCGA-EE-A29H        TCGA-EE-A29L 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29M        TCGA-EE-A29N        TCGA-EE-A29P        TCGA-EE-A29Q 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EE-A29R        TCGA-EE-A29S        TCGA-EE-A29T        TCGA-EE-A29V 
"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-A4F2 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FS-A4F9        TCGA-FS-A4FC        TCGA-FW-A3I3        TCGA-FW-A3R5 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FW-A3TU        TCGA-GN-A261        TCGA-GN-A262        TCGA-GN-A264 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"   "XQ LOSS MUTATED" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A265        TCGA-GN-A266        TCGA-GN-A267        TCGA-GN-A268 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D77V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  XQ LOSS MUTATED                    1             0
  XQ LOSS WILD-TYPE                 24             1
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  XQ LOSS MUTATED                                                                                          2
  XQ LOSS WILD-TYPE                                                                                       33
                   vv
clus                REGIONAL LYMPH NODE
  XQ LOSS MUTATED                     3
  XQ LOSS WILD-TYPE                 109
D77V3, multiclass
                                                                                          clus
vv                                                                                         XQ LOSS MUTATED
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                          0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
  REGIONAL LYMPH NODE                                                                                    3
                                                                                          clus
vv                                                                                         XQ LOSS WILD-TYPE
  DISTANT METASTASIS                                                                                      24
  PRIMARY TUMOR                                                                                            1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                33
  REGIONAL LYMPH NODE                                                                                    109
D77V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      5    1
  XQ LOSS WILD-TYPE   62  105
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               5                62
  MALE                 1               105
                   vv
clus                 M0  M1 M1A M1B M1C
  XQ LOSS MUTATED     5   0   0   0   0
  XQ LOSS WILD-TYPE 145   2   2   2   2
D77V5, multiclass
                   vv
clus                N0 N1 N1A N1B N2 N2A N2B N2C N3 NX
  XQ LOSS MUTATED    4  0   0   0  0   0   0   0  1  0
  XQ LOSS WILD-TYPE 91  2   7  16  1   4  11   5 15  2
D77V6, multiclass
D77V7, continuous
                   vv
clus                I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  XQ LOSS MUTATED             1       1        1        1        0         0
  XQ LOSS WILD-TYPE           3      16        9       13       19         8
                   vv
clus                STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  XQ LOSS MUTATED           0         0         0          0          0
  XQ LOSS WILD-TYPE        10         8         9          6         18
                   vv
clus                STAGE IIIC STAGE IV
  XQ LOSS MUTATED            1        0
  XQ LOSS WILD-TYPE         22        6
D77V8, 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")
